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The Coot User Manual - MRC Laboratory of Molecular Biology

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1. 170 11 92 7 set display generic object 0 eee eee eee 170 11 92 8 generic obiect As dsplaved p eee eee eee 170 11 92 9 generic obiectAndes 0 cece eee eee ee 170 11 92 10 mumber otgenertec obiects 0 cece eee ee 170 11 92 11 generie obhiect Anfo eee eee 170 11 92 12 generic object has objects p 00 c cee eee eens 171 11 92 13 close generic object 0 cece eee eee eee 171 11 92 14 is closed generic object p 1 0 2 00 cee eee eee eee eee 171 11 92 15 generic object clear 00 c cece eee eee ee 171 11 92 16 generie obhiects gui wrgapper eee eee eee 171 11 93 Molprobity Interface 0 eee eee eee 171 11 93 1 bandle read draw probe dots cece e eee 171 11 93 2 handle read draw probe dots unformatted 171 11 93 3 set do probe dots on rotamers and chis 172 11 93 4 do probe dots on rotamers and chis state 172 11 93 5 set do probe dots post refine o ooocoooccccorocccco 172 11 93 6 do probe dots post rebne atate 172 11 93 7 unmangle hydrogen name 00 eee eee ee eee 172 11 93 8 set interactive probe dots molprobity radius 172 11 93 9 interactive probe dots molprobity radius 172 11 94 Map Sharpening Interface 172 T1941 Sharpen arero ii ebenso GEET bee ea EA 172 11 94 2 set map sharpening scale limit 00 005 173 11 95 Marking Fixed Atom Interface 173 11 95 1 clear all fixed at
2. 65 add dictionary glob extension 65 add extra bond restraint ss 124 add extra restraints to other molecule 196 add key binding see 208 add ligand delete residue copy molecule 70 add ligand search ligand molecule 135 add ligand search wiggly ligand molecule EEN 135 add map glob extension sss 65 add molecule cir 181 add ncs matrixoccHuesregt s b Xe e 158 add omega torsion restriants 119 add planar peptide restraints 118 add simple coot menu menuitem 189 add status bar text cece eee ee eee 80 add Strict nce mattriz 0 158 add Cerninal residue 144 add terminal residue do post refine state 145 add terminal residue using phi psi 144 add Cmp extension to rro 203 218 add to list section texis 211 add Mi dt Ste natn 205 add viev description 133 add view here l eel a 132 add vjewzraw o c iia 132 add view to views panel 190 additional representation by attributes EE 141 additional representation by string 141 align and mutate ees 116 alien to closest chain 117 alignment mismatches gui 191 RE ende er wur 208 another level osib gu tes bea e rn IR 92 another level from map molecule number 93 append dir dir i4 cn i S 204 append dir file 2 c eicere 204 apply ncs to view orientation 78
3. cesses 86 extra params include weight 196 F fascinating clusters gui 193 fffear angular resolution 167 fffear searchl i i ecssesM e pe DURER 166 Zile name directorg 201 file name extension esses ss 203 file name sans extension 204 Zile selector entrg 190 File type coords iia a c 66 fill option menu with coordinates mol OPTIONS is ees ee e Rc REED 188 fill option menu with mol options 188 fill option menu with number options 188 Till partial residues sss 149 filtere era ru LS 187 212 filter fileselection filenames state 66 find aligned residue type 201 find helices ified wees tad eed Las ae see we 161 find nucleic acids local 162 find secondary structure 162 find secondary structure local 162 find strandS tv ik Le as br EE 161 first coords imol nep bte HR Seas 71 first molecule with symmetry displayed 97 e ovs cer phun Cuero hr tes 201 first non trivial name sss 200 first small coords imol ss 71 first unsaved coords imol 71 fit chaih voe is 195 fit protein icu fed ri ts 195 Tit protein uake epecg 195 fit residue range to map by simplex 125 fit to map by random jiggle 175 fit Water8 sl As es 195 fix nomenclature errors ss 125 fle view set h bond
4. 0 0 0085 56 V Validation Graphs 0 cece eee eee eee 58 version number eee eee eee eens 8 VIEW MAT ia gatas 14 W waters findihgi mimar 40 Webipageus id tee baa aed 4 weight real space refinement 27 width bondszs vss sag hse os ae ek ee eee 20 WTC MAP vig esse vie pagent oad pase 54 Writing PDBs c ii 26 Y leg 9 Z Z TOLALION ias he wens ana 6 ZETO OCCUPANCY tidad een 23 DIM ia BE OER EY ESA PCR NI eg 62 ZOOM SHAE i Era we cate Wek dc 7 Function Index Function Index 4coot listener socket sess 199 Fannotations 0 eee ees 201 continue multi refine 195 default ball and stick selection 201 do coot tips flag 06 cee eee eee ee 199 imol jligand link 06 186 interactive probe is K 194 jligand home env 0 cece eee 186 key Dindings coco SE EE 208 pisa command ccc eee eee eee 200 probe command esee 199 reduce command eese 199 to jligand secret file name 186 3 3 letter code gt single letter 213 A a rapper B i i o te si eiii ta rias 197 absOl tify EE 201 accept baton position sse 152 aCcCept Cegularizemnent sss 119 Tee KC E EE EE 181 add ACEON VOM ii ao 133 add annotation here eee 210 add coordinates glob extension 65 add data glob extension
5. 0 00 e eee 76 11 8 27 oet draw map standard Dnes nuse c eee eee ee 76 11 8 28 set solid density surface opacity 00 cee eee eee 76 11 8 29 set flat shading for solid density surface 77 11 9 Interface Preferences 0 00 cece eee ee 77 11 9 1 set scroll by wheel mouse 0c c eee eee eee eee 77 11 9 2 scroll by wheel mouse state 0 6 c cece eee eee 77 11 9 3 set default initial contour level for map 77 11 9 4 set default initial contour level for difference map 77 11 9 5 print view matrix eoa 0 eee eee eee eens 77 11 9 6 get view quaternion internal 0 00 e eee eee 78 11 9 7 set view quaternion 00 cece eee eee eee eee 78 11 9 8 apply ncs to view orientation 0c eee eee eee 78 11 9 9 apply ncs to view orientation and screen centre 78 vil vil 11 9 10 set show origin marker sssseeseeeseeeeseee 78 11 9 11 show origin marker state 0 0 ccc cece eee eee 79 11 9 12 hide modelling toolbar 00 0 cece eee eee 79 11 9 13 sbhow m0odellng toolbar 00 eee eee eee 79 11 9 14 hide main toolbar 00 eee ene eee 79 11 9 15 show main toolbar 0 000 79 11 9 16 show model toolbar all icons 0 0 0 cece eee 79 11 9 17 sbhow m0odet toolbar maim Aeomsg eee ee 79 11 9 18 reattach modelling toolbar 0 0 00 cee eee eee 79 11 9 19 zet model toolbar docked posaition ss usesree
6. 2 2000 67 11 5 1 manage column selector 0 0 e cece eee eee eee 67 11 6 Molecule Info Functions 0 c cece eee eee eee 67 11 6 1 chain n residues 0 0 c cece eee eee eens 67 11 6 2 resname Drom zertal number 0000 eee eee eee 67 11 6 8 seomm Drom sertal number cece eens 68 11 6 4 insertion code from serial number 200000 68 11 60 5 nemodels 2240 Sache cashes td Re Rame 68 1 06 60 xXischalng soisss vend er bbb e ident ute p esee quedes 68 11 6 7 js sobvent chaimn n cece ne 68 11 6 8 TESIS coca a ea eee 69 11 0 9 SOrt chains cre hee eae te sers dete da 69 11 6 10 sort residues aa n a a ao n REA ee 69 11 6 11 remarks dalog 69 11 6 12 pGpmt header secondarv structure Anfo 69 11 6 13 copy molecule 0 ence ees 69 11 6 14 add ligand delete residue copy molecule 70 11 6 15 exchange chain ids for seg ids 0c eee eee 70 11 7 Library and Utility Functions 0 0000 e eee eee 70 Td SCO OLEVENSION ck Sun etus A doe ed Bele 70 11 7 2 SVNETCVISIOD EE 70 11 73 molecule name 0 eene 71 11 7 4 set molecule name eee eee 71 11 7 5 coot r al eXit cinc a ENEE Ed 71 11 7 6 first coords imol 0 0 cece cence eee 71 11 7 7 first small coords imol 00 ccc eee eee eee ees 71 11 7 8 Drot umnsgvecd coorda Amol 0 00 cee eee eee eens 71 11 7 9 mmcif sfs to mtz 6 eee en 71 11 8 Graphics Utility Functions 0 00
7. e define refmac exec e refmac new bin refmac5 6 3 After running refmac several times you may find that you prefer if the new map that refmac creates after refmac refinement is the same colour as the previous one from before this refmac refinement If so use set keep map colour after refmac 1 38 je Coot is idle and ignores all input 39 This is not an ideal feature of course and will be addressed in future Digressive Musing If only computers were fast enough to run Refmac interactively Chapter 5 Modelling and Building which will swap the colours of then new and old refmac map so that the post refmac map has the same colour as the pre refmac map and the pre refmac map is coloured with a different colour 5 32 Running SHELXL Coot can read shelx res files and write ins files and thus one can refine using SHELXL in a convenient manner using the function shelxl refine imol hkl file name the hk1 file name is an optional argument e g shelxl refine 0 Or shelxl refine 0 insulin hkl In the former case coot will presume that there is a SHELX hkl file corresponding to the res file that you read in if there is not coot will print a warning and not try to run shelxl In the latter case you can specify the location of the hk1 file After shelxl has finished coot will automatically read in the resulting res coordinates the fcf file convert the data to mmCIF format and read that which gen
8. moving atoms list Where imol map is an integer number imol is an integer number chain id is a string resno is an integer number ins_code is a string direction atoms list is a SCM moving atoms list is a SCM for the given residue spin the atoms in moving atom list around the bond defined by direction atoms list looking for the best fit to density of mol map map of the first atom in moving atom list Works only with atoms in altconf 12 11 protein db 12 11 1 protein db loops protein db loops imol_coords residue_specs imol_map nfrags function Where imol_ coords is an integer number residue_specs is a const std vector lt coot residue_spec_t gt amp imol map is an integer number nfrags is an integer number Cowtan s protein_db loops Chapter 12 More Seripting Functions 184 12 12 Coot s Hole implementation 12 12 1 hole hole mol start_x start_y start_z end_x end_y end z colour map multiplier function colour map offset n_runs show probe radius graph flag Where e imol is an integer number e start_x is a number e start_y is a number e start_z is a number e end x is a number e end_y is a number e end z is a number e colour map multiplier is a number e colour map offset is a number e n runs is an integer number e show probe radius graph flag is a bool starting piont and end point colour map multiplier and shall the probe radius graph be shown dummy value c
9. and others For data mtz hkl phs cif and for CCP4 maps ext msk and map If you want to add to the extensions the following functions are available e add coordinates glob extension extension e add data glob extension extension e add map glob extension extension e add dictionary glob extension extension where extension is something like mycif If you want the fileselection to be filtered without having to use the Filter button use the scripting function set filter fileselection filenames 1 3 9 2 Filename Sorting If you like your files initially sorted by date rather than lexicographically which is the default use set sticky sort by date 3 9 3 Save Coordinates Directory Some people prefer that the fileselection for saving coordinates starts in the original directory rather than the directory from which they last imported coordinates This option is for them set save coordinates in original directory 1 3 10 Scripting There is an compile time option of adding a script interpreter Currently the options are python and guile It seems possible that in future you will be able to use both in the same executable The binary distribution of Coot are linked with guile others with python Hundreds of commands are made available for use in scripting by using SWIG some of which are documented here Other functions documented less well but descriptions for
10. auto fit best rotamer resno altloc insertion_code chain_id imol_coords function imol_map clash_flag lowest_probability Where e resno is an integer number e altloc is a string e insertion code is a string e chain id is a string e imol_coords is an integer number e imol map is an integer number e clash_flag is an integer number e lowest probability is a number auto fit by rotamer search return the score for some not very good reason clash flag determines if we use clashes with other residues in the score for this rotamer or not It would be cool to call this from a script that went residue by residue along a newly built chain now available 11 69 5 set auto fit best rotamer clash flag set auto fit best rotamer clash flag i function Where i is an integer number set the clash flag for rotamer search And this functions for pre setting the variables for auto fit best rotamer called in teractively using a graphics info t function 0 off 1 on 11 69 6 n rotamers n rotamers imol chain id resno ins_code function Where e imolis an integer number e chain id is a string e resno is an integer number e ins code is a string return the number of rotamers for this residue return 1 on no residue found 11 69 7 set residue to rotamer number set residue to rotamer number imol chain id resno ins_code function rotamer number Where e imol is an integer number e chain id is a string Ch
11. read pdb all procedure read pdb all reads all the pdb files in the current directory string gt list of strings str procedure Return a list if str is a string else return append dir file dir name file name procedure In a laughable attempt to minimise system dependence append dir dir dir name sub dir name procedure Similarly attempting to minimise system dependence directory as file name dir procedure remove any trailing s is directory file name procedure return t or f depending on if file name which must be a string is a directory coot mkdir dir name procedure return f if dir name is a file or we can t do the mkdir directory files dir procedure The following functions from PLEAC guile version thereof of course Return a list of files in the given directory Chapter 13 Scheme Scripting Functions glob pat dir return a list of file names that match pattern pat in directory dir view matrix return the view matrix useful for molscript perhaps view quaternion return the view quaternion add view position quaternion zoom view name Return the view number matrix gt quaternion Convert a view matrix to a view quaternion to set Coot view internals set view matrix m00 m10 m20 m01 m11 m21 m02 m12 m22 Set the view matrix using matrix gt quaternion Useful for using a view matrix from another program perhaps molecule centre imol Return the molecule centre as a list of 3 numbers
12. write molecule number imol s residue range as a PDB to file file name 11 19 3 quick save quick save function save all modified coordinates molecules to the default names and save the state too Chapter 11 Scripting Functions 11 20 Refmac Functions 11 20 1 set refmac counter set refmac counter imol refmac_count function Where e mol is an integer number e refmac_count is an integer number set counter for runs of refmac so that this can be used to construct a unique filename for new output 11 20 2 refmac name refmac name imol function Where mol is an integer number the name for refmac Returns a stub name used in the construction of filename for refmac output 11 20 3 swap map colours swap map colours imoll imol2 function Where e imoll is an integer number e imol2 is an integer number swap the colours of maps swap the colour of maps imoll and imol2 Useful to some after running refmac so that the map to be build into is always the same colour 11 20 4 set keep map colour after refmac set keep map colour after refmac istate function Where istate is an integer number flag to enable above call this with istate 1 11 20 5 keep map colour after refmac state keep map colour after refmac state function the keep map colour after refmac internal state Returns 1 for yes 0 for no Chapter 11 Scripting Functions 11 21 Symmetry Functions 11 21 1 set symmetry size set symmetry size f funct
13. 10 It uses sphere refinement The refinement map must be set At the end show the new weight in the status bar Seems to take about 5 rounds print sequence imol procedure Print the sequence of molecule number mol This is not really a util perhaps it should be somewhere else Chapter 13 Scheme Scripting Functions 208 pir file name gt pir sequence pir file name procedure simple utility function to return the contents of a file as a string associate pir file imol chain id pir file name procedure Associate the contents of a PIR file with a molecule graphics comma key pressed hook procedure comma key hook graphics dot key pressed hook procedure dot key hook key bindings procedure a list of code key name thunk e g 103 g Goto Blob blob under pointer to screen centre add key binding name key thunk procedure Add a key binding with a given name key e g x or S and the function to run a thunk when that key is pressed graphics general key press hook key procedure general key press hook not for public use read vu file procedure Function requested by Mark White read XtalView and maybe other vu files and convert them into generic objects Pass the filename and an object name e g read vu file axes vu axes Returns nothing interesting residues matching criteria imol residue test func procedure Return a list of residues each of which has a return value at the start
14. 199 open coot listener socket with timeout 199 output atom info as text 126 overlay my ligands s s ssssssse 209 P parse check db 1l lesa Din 192 parse pisa assemblies sss 200 parse pisa interfaces ssssss 200 pdbe get pdb and sfs cif 185 pdbe latest releases gui 185 Function Index E Ob E 143 DepfLip active residue 196 phosphorylate active residue 209 pir file name gt pir sequence 208 Dilsa assenblies ml 200 pisa handle sxml molecule 200 pisa interactyOn u das 175 place helix here e tue adele nee 161 Dlace sttand here cc cece e ees 161 place strand here dialog 161 place text 12 215 1l b6 EECHER 174 pointer atom molecule ssss 151 post display control window 114 post go to atom WindoW sssssssssss 113 Dost Ligand fir eui 195 post manipulation hook sss 201 post model fit refine dialog 81 post other modelling tools dialog 81 post python scripting windoW 118 post scheme scripting windoW 118 post scriptingWiddoW oo o oooooomooooo 118 Ch EE 198 LKE Geh 198 POVTAN MEET eege ii 198 pre release oi icicle kd eee rd 201 prefer python co gg ve EAR DEIIE YR 64 eh ee eeng ee v iD EIER 200 print all history in python 100 prin
15. draw molecule number imol with bonds in secondary structure representation 11 62 15 graphics to rainbow representation graphics to rainbow representation imol function Where mol is an integer number draw molecule number imol in Jones Rainbow 11 62 16 graphics to b factor representation graphics to b factor representation imol function Where mol is an integer number draw molecule number imol coloured by B factor 11 62 17 graphics to b factor cas representation graphics to b factor cas representation imol function Where mol is an integer number draw molecule number imol coloured by B factor CA ligands 11 62 18 graphics to occupancy representation graphics to occupancy representation imol function Where mol is an integer number draw molecule number imol coloured by occupancy 11 62 19 graphics molecule bond type graphics molecule bond type imol function Where mol is an integer number what is the bond drawing state of molecule number imol 11 62 20 set b factor bonds scale factor set b factor bonds scale factor imolf function Where e imol is an integer number e f is a number scale the colours for colour by b factor representation Chapter 11 Scripting Functions 141 11 62 21 change model molecule representation mode change model molecule representation mode up_or_down function Where up_or_down is an integer number change the representation of the model molecule closest to the centre
16. esses 165 11 86 5 assign sequence from string lesse 165 11 86 6 delete all sequences from molecule nusnausnnnnnna 165 11 86 7 delete sequence by chain id 0 0 eee eee eee 166 11 87 Surface Interface 166 VESTLE do surface atic a EEN ees D 166 11 87 2 set transparent electrostatic surface 166 11 87 3 get electrostatic surface opacity 00 e ee eee 166 11 88 PRESA titi e Ai e 166 11 88 1 fffear search ioeie a a E E E E E 166 11 88 2 set fffear angular resolution 0 00 eee 167 11 88 3 fffear angular resolution 0 000 cece eee eee 167 11 89 Remote Control 167 11 89 1 make socket listener maybe 0 000 eee eee 167 11 90 Display Lists for Maps 167 11 90 1 set display lists for maps 0 e eee eee eee 167 11 90 2 display lists for maps state sse eee eee ee 167 11 91 Browser Interface 167 11 91 1 browser url 167 11 91 2 set browser interface 0 cece eee ee eee 167 11 91 38 handle online coot search request ee eee eee 168 11 92 Generic Objects 0 cece ence seh 168 11 92 1 new generic obieck number cece eee eee 168 11 92 2 to generic object add line 00 e eee eee eee 168 11 92 3 to generic object add dashed line 204 168 11 92 4 to generic object add point 0 cee eee eee ee 169 11 92 5 to generic object add arc cece eee eee 169 11 92 6 to generic object add display list handle
17. page 42 sd you can search for many different ligand types Chapter 5 Modelling and Building 5 21 Flip Ligand Sometimes a ligand is placed more or less in the correct position but the orientation is wrong or at least you might want to explore other possible orientation To do that easily a function has been provided flip ligand imol chain id residue number This will flip the orientation of the residue around the Eigen vector corresponding to the largest Eigen value exploring 4 possible orientations This function has been further wrapped to provide flipping for the active residue flip active ligand This function can easily be bound to a key 5 22 Find Waters As with finding ligands you are given a chose of maps protein masking atoms A final selection has to be made for the cut off level note that this value is the number of standard deviation of the density of the map before the map has been masked The default sigma level water positions must have density above this level is set for a 2Fo Fc style map If you want to use a difference map you must change the sigma level typically to 3 sigma otherwise you run the risk of fitting waters to difference map noise peaks Then the map is masked by the masking atoms and a search is made of features in the map about the electron density cut off value Waters are added if the feature is approxi mately water sized and can make sensible hydrogen bonds to the p
18. return 1 if all atoms of the specified residue are HETATMs else return 0 If residue not found return 1 11 8 21 het group n atoms het group n atoms comp id function Where comp_id is a string return the number of non hydrogen atoms in the given het group comp id Return 1 on comp id not found in dictionary 11 8 22 replace fragment replace fragment imol target imol fragment atom selection function Where e imol target is an integer number e imol_fragment is an integer number e atom selection is a string replace the parts of molecule number imol that are duplicated in molecule number imol frag 11 8 23 copy residue range copy residue range imol target chain id target imol reference function chain id reference resno_range_start resno range end Where e imol target is an integer number e chain id target is a string e mol reference is an integer number chain id reference is a string e resno_range_start is an integer number e resno_range_end is an integer number copy the given residue range from the reference chain to the target chain resno Tango start and resno range end are inclusive Chapter 11 Scripting Functions 11 8 24 clear and update model molecule from file clear and update model molecule from file molecule number function file name Where e molecule number is an integer number e file name is a string replace pdb Fail if molecule number is not a valid model molecule Re
19. returns a rotation translation operator which can be applied to other molecules and maps Here imol ligand is the molecule number of the ligand which is presumed to be a a molecule on its own Coot simply takes the first residue that it finds imol ref chain id ref resno ref collectively describe the target position for the moving imol ligand molecule The convenience function overlay my ligands imol mov chain id mov resno mov imol ref chain id ref resno ref wraps overlap ligands The GUI for the function can be found under Extensions gt Modelling gt Supperpose Ligands Chapter 4 Coordinate Related Features 26 4 23 Writing PDB files As well as the GUI option File Save Coordinates there is a scripting options avail able write pdb file imol pdb file name which writes the imolth coordinates molecule to filename To write a specific residue range write residue range to pdb file imol chain id start resno endresno pdb file name Chapter 5 Modelling and Building 27 5 Modelling and Building The functions described in this chapter manipulate extend or build molecules and can be found under Calculate Model Fit Refine When activated the dialog stays on top of the main graphics window Some people think that this is not always desirable so this behaviour can be undone using set model fit refine dialog stays on top 0 5 1 Regularization and Real Space Refinement Coot will read the
20. ssssususesusen rr nnrerosere 37 5 17 3 Mutating to a Non Standard Besidue 38 5 17 4 Mutate and Autofit 0 eee cece eee eee 38 5 17 5 Renumbering a cece ene ene 38 5 18 Importing Lignds Monomers 22 ecd eevee n ehe 38 5 19 Ligand from SMILES stmngs 0 0 cece eee eee eee 38 5 20 Eid Ligands rr ts 39 5 20 1 Flexible Ligands 0 0 cece cence eee eee 39 111 5 20 2 Adding Ligands to Model 39 5 21 Flip Ligand ii SA A ae 40 5 22 Wind Waters a eet e E EE 40 5 22 1 Refinement Failure 0 0 eee cece eee eee 40 510222 Bl cita da A RA aaa 41 5 23 Add Terminal Residue 0 0 ccc e cece eee eens 41 5 24 Add OXT Atom to Residue 0 00 cece eee eee eens 41 5 25 Add Atom at Pointer 00 cece cece eens 42 526 Place Helix harer wae ee bese tds 42 5 27 Building Ideal DNA and BNA e eee eee ee 42 5 28 Merge Molecules 2 0 cece cece eee eee eens 42 5 29 Temperature Factor for New Atoms cee eens 42 5 30 Applying NCS dite 43 5 31 Running Befiumac 0 00 cece eee nen 43 5 32 Running SHELXL 0 cece eens 44 5 33 Clear Pending Dicks 44 5 94 Delete was iaa A a era RA 44 5 35 Sequence Assignment 00 ccc rr 45 5 36 Building Links and Loop 45 5 37 Fill Partial Residues 00 c cece eee eens 45 5 38 Changing Chain Die 45 5 39 Setting Oecupancdes 0 0 cece eee een 46 5 40 Fix Nomenclature kor 46 5 41 Rotamer Fix Whole Protei
21. Chapter 11 Scripting Functions 163 11 84 New Molecule by Section Interface 11 84 1 new molecule by residue type selection new molecule by residue type selection imol residue_type function Where e imol is an integer number e residue type is a string create a new molecule that consists of only the residue of type residue type in molecule number imol Returns the new molecule number 1 means an error 11 84 2 new molecule by atom selection new molecule by atom selection imol atom selection function Where e imolis an integer number e atom selection is a string create a new molecule that consists of only the atoms specified by the mmdb atoms selection string in molecule number imol Returns the new molecule number 1 means an error 11 84 3 new molecule by sphere selection new molecule by sphere selection imolx y zr allow partial residues function Where e imol is an integer number e risanumber e y is a number e zis a number e ris a number e allow_partial_residues is an integer number create a new molecule that consists of only the atoms within the given radius r of the given position Returns the new molecule number 1 means an error 11 85 RNA DNA 11 85 1 ideal nucleic acid ideal nucleic acid RNA or DNA form single_stranged_flag sequence function Where e RNA_or_DNA is a string Chapter 11 Scripting Functions 164 e form is a string e single stranged flag is an integer number e
22. a residue range or a whole chain Note that the target res type is a char not a string or a char So from the scheme interface you d use for example hash backslash A for ALA Returns 1 on success 0 on failure 11 71 9 set residue type chooser stub state set residue type chooser stub state istat function Where stat is an integer number set a flag saying that the residue chosen by mutate or auto fit mutate should only be added as a stub mainchain CB 11 72 Pointer Atom Functions 11 72 1 create pointer atom molecule maybe create pointer atom molecule maybe function Return the current pointer atom molecule create a pointer atom molecule if necessary i e when the user has not set it 11 72 2 pointer atom molecule pointer atom molecule function Return the current pointer atom molecule 11 73 Baton Build Interface Functions 11 73 1 set baton mode set baton mode i function Where i is an integer number toggle so that mouse movement moves the baton not rotates the view 11 73 2 try set draw baton try set draw baton i function Where i is an integer number draw the baton or not Chapter 11 Scripting Functions 152 11 73 3 accept baton position accept baton position function accept the baton tip position a prime candidate for a key binding 11 73 4 baton try another baton try another function move the baton tip position another prime candidate for a key binding 11 73 5 shorten ba
23. but with some corners cut to make things more or less interactive The algorithm uses the shape of the density around the C beta position to estimate the probability of each sidechain type at that position The function is accessed via the Extensions gt Dock Sequence menu item First a sequence should be assigned from a PIR file to a particular chain id and model number Secondly Extensions gt Dock Sequence gt Dock Sequence on this fragment Choose the model to build on and then Dock Sequence If all goes well the model will be updated with mutated residues and undergo rotamer seach for each of the new residues If the sequence alignment is not sufficiently clear then you will get a dialog suggesting that you extend or improve the fragment 5 12 Rotamers The rotamers are generated from the backbone independent sidechain library of the Richardsons group The m t and p stand for minus 60 trans 180 and plus 60 There is one letter per x angle Use keyboard and to cycle round the rotamers 5 12 1 Auto Fit Rotamer Auto Fit Rotamer will try to fit the rotamer to the electron density Each rotamer is generated rigid body refined and scored according to the fit to the map Fitting the second conformation of a dual conformation in this way will often fail the algorithm will pick the best fit to the density ignoring the position of the other atoms The algorithm doesn t know if the
24. c eee eee eee 72 11 8 1 zet do antt albaaing 0 eee eens 72 11 8 2 do anti aliasing state 0 eee eens 72 11 8 8 set do GL lighting 2 0 0 0 cece eee eee 72 11 84 do GL lighting state 0 cece eee 72 11 8 5 use graphics interface state csse 72 11 8 6 start erapbies Anterface 0 cece eee eee 72 TB rfesel View ii iy ae he se Quen Rs 72 11 88 graphics n molecules 0 c cece eee eens 73 11 8 9 toggle idle spin function 00 eee eee eee eee 73 11 8 10 Toggle Adle rock Punction 0 00 cece eee eee ee 73 11 8 11 set rocking factors oooocccoocccccnnnncccrr eens 73 11 8 12 set idle function rotate angle 0 cece eee eee 73 11 8 13 handle read draw molecule 0 0 c cece eee 73 11 8 14 set convert to v2 atom naMes 0 eee eee eee eee 73 11 8 15 handle read draw molecule with recentre 74 11 8 16 handle read draw molecule and move molecule here 74 Il 8 I7 read Pd ee egre bene ee EDS 74 11 8 18 assten hetatmsg eee eee eens 74 11 8 19 hetify residue 0 ccc eee ene eh 74 11 8 20 residue has hetatms sese eee 75 11 8 21 bet eroup n atomsg eee eee 75 11 8 22 replace fragment 00 75 11 8 23 copy residue range 0 0 ccc eene 75 11 8 24 clear and update model molecule from file 76 11 8 25 screendump image 0 cece eee eee eee eee 76 11 8 26 set draw solid density surface
25. e for a difference map You can change these using Edit gt Map Parameters or by using the Properties button of a particular map in the Display Control Display Manager window 6 4 Map Extent The extent of the map can be set using the GUI Edit gt Map Parameters gt Map Radius or by using the scripting function e g set map radius 13 2 6 5 Map Contour Scrolling Limits Usually one doesn t want to look at negative contour levels of a map so Coot has by default a limit that stops the contour level going beyond less than 0 To remove the limit set stop scroll iso map 0 for a 2Fo Fc style map set stop scroll diff map 0 for a difference map To set the limits to negative e g 0 6 levels set stop scroll iso map level 0 6 and similarly set stop scroll diff map level 0 6 where the level is specified in e 4 6 6 Map Line Width The width of the lines that describe the density can be changed like this set map line width 2 The default line width is 1 6 7 Dynamic Map colouring By default maps get coloured according to their molecule number The starting colour i e for molecule 0 is blue The colour of a map can be changed by Edit gt Map Colour The map colour gets updated as you change the value in the colour selector Use OK to fix that colour As subsequent maps are read they are coloured by rotation round a colour wheel The default colour map step is 3
26. e sigma CH off is a number find waters Chapter 11 Scripting Functions 137 11 61 2 move waters to around protein move waters to around protein imol function Where mol is an integer number move waters of molecule number imol so that they are around the protein Returns the number of moved waters 11 61 3 move hetgroups to around protein move hetgroups to around protein imol function Where mol is an integer number move all hetgroups including waters of molecule number imol so that they are around the protein 11 61 4 max water distance max water distance imol function Where mol is an integer number return the maximum minimum distance of any water atom to any protein atom used in validation of move waters to around protein funtion 11 61 5 set water check spherical variance limit set water check spherical variance limit f function Where f is number set the limit of interesting variance above which waters are listed otherwise ignored default 0 12 11 61 6 set ligand water to protein distance limits set ligand water to protein distance limits fl f2 function Where e f isa number e f2 is a number set ligand to protein distance limits fl is the minimum distance f2 is the maximum distance 11 61 7 set ligand water n cycles set ligand water n cycles i function Where i is an integer number set the number of cycles of water searching Chapter 11 Scripting Functions 11 61
27. e tx is a number e ty is a number e tz is a number e pre_shift_to_origin_na is an integer number e pre_shift_to_origin_nb is an integer number e pre_shift_to_origin_nc is an integer number create a new molecule molecule number is the return value from imol but only for atom that match the mmdb_atom_selection_string The rotation translation matrix components are given in orthogonal coordinates Allow a shift of the coordinates to the origin before symmetry expansion is aplied Pass as the name in and a name will be constructed for you Return 1 on failure 11 21 15 new molecule by symop new molecule by symop imol symop string pre_shift_to_origin_na function pre_shift_to_origin_nb pre_shift_to_origin_nc Where e imol is an integer number e symop_string is a string e pre_shift_to_origin_na is an integer number e pre_shift_to_origin_nb is an integer number e pre_shift_to_origin_nc is an integer number create a new molecule molecule number is the return value from imol 11 21 16 n symops n symops imol function Where mol is an integer number return the number of symmetry operators for the given molecule return 1 on no symmetry for molecule or inappropriate imol number Chapter 11 Scripting Functions 100 11 21 17 set space group set space group imolspg function Where e imol is an integer number e spg is a string set the space group for a coordinates molecule for shelx FA pdb files there is no
28. graphics general key press hook 208 graphics molecule bond type 140 Sraphice n molecules erene 73 graphics to b factor cas representation O EE 140 graphics to b factor representation 140 graphics to bonds no waters representation Get eer naa Doce ie us 139 graphics to bonds representation 139 graphics to ca plus ligands representation exo outs sedat tpe du eet E Sui te de 139 graphics to ca plus ligands sec struct representation sse 140 graphics to ca representation 139 graphics to occupancy representation 140 graphics to rainbow representation 140 graphics to sec struct bonds representation DEE 140 Buess Cefinement uap 207 H bandle cpns data file sns 128 handle cns data file with cell 128 handle drag and drop string 184 handle online coot search request 168 bandle read ccpi map 0c eee 110 handle read draw molecule 73 handle read draw molecule and move molecule here cc cece cece 74 handle read draw molecule with recenter EE 198 handle read draw molecule with recentre 74 handle read draw probe dots 171 handle read draw probe dots unformatted A A Metal EE 171 handle smilesgo scinn cciias pinea tenis 187 hardware stereo angle factor state 105 hardware stereo mode cece eee eee 104 has unit cell state eee 97 have unsaved changes p sssssrssrrreso 82 het group
29. max water distance esses 137 MONDE a lees E NE 202 merge Solvent chains 209 min max residues from atom specs 191 missing atoms gui 0 cece eee eee 189 mmcif sfs to mtz sides eh eee 71 model a0olecule Lier en 202 mnodel resolution ic e o a PR 86 mol js active ve A 115 mol is displayed rl en eneh IRR 115 molecule centre 5 d ehre da Ree Eder 205 molecule centtesg gul ss 188 molecule chooger gui ss 189 molecule chooser gui generic 188 molecule has hydrogens 201 Molecule name oia dedu 71 molecule number list eese 201 molecules matching criteria 195 MONO Modenie aie e na E ad ce 104 monomer molecule from 3 let code 193 most recently created file 201 move hetgroups to around protein 137 move molecule here o ooooooooommmmmmo 205 move molecule to screen center 205 move molecule to screen centre 205 move waters to around protein 137 mtz fp for map cenae a 93 mtz hklin for map nep vv 93 mtz phi for mapc iieile i E e I ERES 93 mtz use weight for map ss 94 mtzveigbt for map 6 cece eee 94 m lti chickeni cb oye daha Lakes 209 multi mutate csiveeeiee r olvag see es 213 mnulti read pdb nceuliewesscksteWwertrvsuwrs 204 multi residue torsion fit scm 179 MULA ii ES Penne Ga er E 149 mutate and auto fit ssssssss 2
30. they shouldn t be considered typically 0 01 1 You can change the auto fit rotamer fitting algorithms using set rotamer search mode mode where mode is one of ROTAMERSEARCHAUTOMATIC ROTAMERSEARCHLOWRES i e Backrub Rotamers vide infra or ROTAMERSEARCHHIGHRES the conventional high resolution method using rigid body fitting By default the auto fit rotamer method is ROTAMERSEARCHAUTOMATIC 5 12 1 1 Backrub Rotamers By default Auto Fit Rotamer will switch to Backrub Rotamer mode when fitting against a map of worse than 2 7 This search mode moves the some atoms of the mainchain of the neighbouring residues After rotation of the central residue and neighbouring atoms around the backrub vector the individual peptides are back rotated along the peptide axis so that the carbonyl oxygen are placed as near as possible to their original position The Ramachandran plot is not used in this fitting algorithm 5 12 2 De clashing residues Sometimes you don t have a map but nevertheless there are clashing residues for example after mutation of a residue range and you need to rotate side chains to a non clashing rotamer There is a scripting interface de clash imol chain id start resno end resno start resno is the residue number of the first residue you wish to de clash end resno is the residue number of the last residue you wish to de clash imol is the molecule number of the coordinates molecule
31. use Edit Restraints to check and modify the restraints group Likewise for modified RNA DNA nucleotides you need to specify the group as RNA or DNA as appropriate 5 17 4 Mutate and Autofit The function combines Mutation and Auto Fit Rotamer and is the easiest way to make a mutation and then fit to the map You can currently only Mutate and Autofit protein residues i e things with a rotamer dictionary 5 17 5 Renumbering Renumbering is straightforward using the renumber dialog available under Calculate gt Renumber Residue Range There is also a scripting interface renumber residue range imol chain id start res no last resno offset 5 18 Importing Lignds Monomers You can import monomers often ligands using File Get Monomer by providing the 3 letter code of your monomer ligand The resulting molecule will be moved so that it placed at the current screen centre Typically when you are happy about the placement of the ligand you d then use Merge Molecules to add the ligand monomer to the main set of coordinates This procedure creates a pdb file monomer XXX pdb and a dictionary file libcheck_XXX cif in the directory in which Coot was started A future invocation of Get Monomer uses these file so that the monomer appears quickly 0 5 19 Ligand from SMILES strings Similarly you can generate ligands using File SMILES and providing a SMILES string and a code for the residue name this is you
32. 0 black 3 18 Unit Cell If coordinates have symmetry available then unit cells can be drawn for molecules Draw gt Cell amp Symmetry gt Show Unit Cell 3 19 Rotation Centre Pointer There is a pink pointer at the centre of the screen that marks the rotation centre The size of the pointer can be changed using Edit Pink Pointer Size or using scripting commands set rotation centre size 0 3 3 20 Orientation Axes The green axes showing the orientation of the molecule are displayed by default To remove them use the scripting function set draw axes 0 3 21 Pointer Distances The Rotation Centre Pointer is sometimes called simply Pointer One can find distances to the pointer from any active set of atoms using Pointer Distances under Measures If you move the Pointer e g by centering on an atom and want to update the distances to it you have to toggle off and on the Show Pointer Distances on the Pointer Distances dialog 3 22 Crosshairs Crosshairs can be drawn at the centre of the screen using either the C key in graphics window or Draw gt Crosshairs The ticks are at 1 54 2 7 and 3 8 18 I find a clipping level of about 3 5 to 4 comfortable for viewing electron density maps it is a little thinner than the default startup thickness 19 Inspired by PyMol Yep sure was 20 and C again to toggle them off Chapter 3 General Features 17 3 23 3D Annotations
33. 109 Skip to next ncs chain sees 191 slash start o sits AREE UTD 204 smiles gui exl xA ieu 187 Smootbh scroll do zoom s s s ssesssso 127 SODA AOS dit d Ke a 69 SoOrt residues muii ver ee 69 Spinssearch reia Mids a aces 183 spin zoom trans sss ee ns 131 start graphics interface 72 start jligand listener oooooommmoo o 186 Stepped refine protein 195 stepped refine protein for rama 195 stepped refine protein with refine func Ls m 195 stereo mode state sse 104 string list of strings 204 211 string append with spaces 202 string append with string 203 string concatenate s 204 212 string member os iride Jdete bistra bestest 202 Strip ertenuslon 203 211 strip leading spaces 192 203 STEP PAI ina ants hes eats in See 204 Strip spaces de c oc e tea EE 203 Suck uodel fit dialog 80 SUPCLPOSE mira is Weeer A as 156 superpose with atom selection 156 superpose with chain selection 156 SVn revislOn i eb lix ADR rs ee 70 swap map colourS sse 95 symmetry as calphas sees 96 symmetry molecule rotate colour map state ui keubcug niet wii URL A F 97 T target auto weighting value 207 POD DDR 193 teb2 a ds 193 Function Index TIPS ds AAN 198 ET AE EE 212 to generic object add arc 169
34. 11 16 3 set map sampling rate 0 2 0 0 cece eee eee ee 87 11 16 4 get map sampling rate ooooccooocccconnccccn eee 87 11 16 5 change contour level 0 00 eee eee eens 87 11 16 6 set Jast map contour Jevel 0 00 c eee eee eee eee 88 11 16 7 set last map contour level by sigma esses 88 11 16 8 zet stop scroltdftman nrn 88 11 16 9 set stop scroll iso map 2 6 6 cece eee I 88 11 16 10 set stop scroll iso map level 0 02 eee 88 11 16 11 set stop scroll diff map level 0 00 e eee eee 88 11 16 12 set residue density fit scale factor ooooooocccomm 88 11 17 Density Functions 0 cece eee e 89 11 17 1 zet map Dne a dth eee eee 89 11 17 2 map line width state 00 0 cece eee 89 11 17 38 make and draw map eee eee eee eens 89 11 17 4 make and draw map with refmac params 89 11 17 56 make and draw map with reso with refmac params 90 11 126 valid labels i iii E IMMER 90 11 17 7 auto read make and draw maps 0 eee eee eee 91 11 17 8 set auto read do difference map too 00 0000s 91 11 17 9 auto read do difference map too state 00 91 11 17 10 set auto read column labels 000 cece e eee 91 11 17 11 set map radius 00 a eee eee 91 11 17 12 set density size 2 16 cee eee eee 91 11 17 13 set display intro string 0 0 eee eee eee 92 11 17 14 get map radius 06 ene nee 92 11 17 15 s
35. 12 export maps Qs l9 Rv dep pe 54 EYC TIED EE dede hits 48 F file name filtering eee eee oo 11 fill partial residues 00 e eee eee eee 45 findligand ista ran Ven SER 63 flip DER ste ie ol EES EEN 36 fragment direction change 33 frame EEN 17 G NA 4 GLN and ASN B factor Outliers 57 uo M rt TET 21 au 60 RUE 12 Concept Index H helix placement 0 ccc cece cece eee ees 42 Id OS ca ao mee MK S 20 I initialization Die 12 L Least Squares tts 25 ligand orientation s ssusrssrrrrerrrrre 40 ligand torsion angles 36 ligand overlay ee 2 2 nen ono eena ENEE 25 ligands sse bi RP dE RS 38 39 ligands flexibles comus R ianen pal 39 M TK 33 mainchain tOrsionsS eee eee ee eee eee 33 map box road 50 map changing for refinement building 30 Map extent oer we AE eb X Ed 50 map line width 50 map scrolling woo li wage bee 6 map transformation sees 53 MASKS condone ka eee AA IS 52 m ar B lactor tacna ac 24 median B factor 0c cece eee ee eee eee 24 merge molecules 00 e eee eee eee ee 42 missing symmetry 0 23 mmCIF dictionary sees eese 28 modelling toolbar 0 cece eee eee eee 11 modified labels 0 cece eee ee eee eee 47 molecule Centre 46 molecule number 8 Molprobity Tools 57 MONOMETS A imajen EN 38 MOUSE nata EE 2 mouse buttons cece eee eee eee eee 5 moving ligands
36. 122 set refine with torsion restraints 120 set refinement immediate replacement 119 set refinement move atoms with zero OCCUPANCY hse kee vs herr ctu eet 81 set refinement refine per frame 122 set refmac counter ess 0c cece 95 set renderer show atoms 155 set reset b factor moved atoms 108 set residue density fit scale factor 88 Set residue name cece eee 109 set residue selection flash frames number a EE 119 set residue to rotamer number 148 set residue type chooser stub state 151 set rigid body fit acceptable fit fraction MES 144 set rocking factors ccce 73 set rotamer auto fit do post refine 150 set rotamer check clashes 147 set rotamer lowest probability 147 set rotamer search mode 147 set rotamer selection dialog position 106 set rotate translate dialog position 106 set rotation center esses 198 set rotation center size ss 198 set run state file status 101 set save state file name 101 Function Index set scroll by wheel mouse 77 Set Scroll sbeel uap 84 Set Scrollable mnap srren 84 set secondary structure restraints type A arte cue D t I tetro Fa RS 123 set show chiral volume errors dialog 123 set show environment distances 126 set show environment distances
37. 2 2 Reading CIF data There are several maps that can be generated from CIF files that contain observed Fs calculated Fs and calculated phases e read cif data with phases fo alpha calc cif file name Calculate an atom map using F bs and a alc 1 e g it s a directory or a coordinate filename Chapter 6 Map Related Features e read cif data with phases 2fo fc cif file name Calculate an atom map us ing F bs F alc and a alc e read cif data with phases fo fc cif file name Calculate an difference map using F bs F alc and ole 6 2 3 Reading PHS data There are 2 ways to read data by scripting read phs and make map using cell symm phs file name space group name a b c alpha beta gamma read pdb and make map with reso limits imol previous phs file name reso limit low reso limit high The first specifies the cell explicitly and alpha beta and gamma are specified in degrees The second form allows the specification of resolution limits and takes the cell and symmetry from a previous molecule typically a pdb file 6 3 Map Contouring Maps can be re contoured using the middle mouse scroll wheel buttons 4 and 5 in X Win dow System TM terminology Scrolling the mouse wheel will change the map contour level and the map it redrawn If you have several maps displayed then the map that has its contour level changed can be set using HID gt Scrollwheel gt Attach scroll wheel to which map If there is only one map displaye
38. 4 324 337 which is quite likely at first since coot has no knowledge of where the chain has been and cannot score according to geometric criteria 1 Chapter 5 Modelling and Building Occasionally every point is not where you want to position the next atom In that case you can either shorten or lengthen the baton or position it yourself using the mouse Use b on the keyboard to swap to baton mode for the mouse Baton built atoms are placed into a molecule called Baton Atom and it is often sensible to save the coordinates of this molecule before quitting coot If you try to trace a high resolution map 1 5 or better you will need to increase the skeleton search depth from the default 10 for example set max skeleton search depth 20 Alternatively you could generate a new map using data to a more moderate resolution 2 the map may be easier to interpret at that resolution anyhow The guide positions are updated every time the Accept button is clicked The molecule name for these atoms is Baton Build Guide Points and is is not usually necessary to keep them 5 7 1 Undo There is also an Undo button for baton building Pressing this will delete the most recently placed Co and the guide points will be recalculated for the previous position The number of Undo s is unlimited Note that you should use the Undo button in the Baton Build dialog not the one in the Model Fit Refine
39. 4 2 Atom Info EE 19 4 3 Atom Labeling 1 bene a MA ue xxi ERE 19 AA Atom Golo umnmng eie eter tM rA esee ep Ik 19 4 5 Bond Parameters osceni nis eiert Pea nn 20 4 5 1 Bond Thickness 0 0 0 cece cece eect eee ees 20 4 5 2 Display Hydrogens 0 cece cee eee eee 20 4 5 3 NOS Ghosts Coordinates 00 sene 20 ADA NOS MapStats EK E UST SERRA AE 21 4 5 5 Using Strict NOR 21 4 6 Download coordimnates nee 21 4 7 Get Coordinates and Map from EI 21 4 8 Save Coordinates een 22 4 9 Setting the Space Group 22 4 10 Anisotropic Atoms 0 00 ccc cece eee eee eens 22 ALT Symmetry ai E ham E Een ZE 22 4 11 1 Missing symmetry 0 eee eee eee 23 4 12 Sequence Views sce iene ete e eU ERE adh eke 23 4 18 Print Sequences sic ssa as Ca dats coed 23 4 14 Environment Distances 00 eee eee eee ee 23 4 15 Distances and Angles 0 00 e cece eee eee eee ee 23 4 16 Zero Occupancy Marker 0 0 cece eee eee eee 23 LIT Atomic RE due a ERR 23 11 4 18 Ball and Stick Representation 0 0 ccc eee eee eee 24 4 19 Mean Median Temperature Hactorg 00 2 eee ee ee 24 4 20 Secondary Structure Matching GM 24 4 21 Least Squares Hung 25 4 22 Ligand Overlaying 0 00 cece eee n 25 4 23 Writing PDB files coetus ceR UC eR INSIDE E Ret ee 26 Modelling and Building 27 5 1 Regularization and Real Space Bebnement 27 b Dictionary ju veesc Mee eee Boney Bie tas 28 5 1 2 S
40. 8 execute find blobs execute find blobs imol_model imol_for_map cut_off interactive flag Where e imol model is an integer number e mol_for_map is an integer number e culi off is a number e inleractive flag is an integer number find blobs 11 62 Bond Representation 11 62 1 set default bond thickness set default bond thickness t Where is an integer number set the default thickness for bonds e g in coot 11 62 2 set bond thickness set bond thickness imolt Where e imol is an integer number e Lisa number set the thickness of the bonds in molecule number imol to t pixels 11 62 3 set bond thickness intermediate atoms set bond thickness intermediate atoms t Where t is a number set the thickness of the bonds of the intermediate atoms to t pixels 11 62 4 set default representation type set default representation type type Where type is an integer number set the default represenation type deafult 1 11 62 5 get default bond thickness get default bond thickness get the default thickness for bonds 138 function function function function function function Chapter 11 Scripting Functions 139 11 62 6 set draw zero occ markers set draw zero occ markers status function Where status is an integer number set status of drawing zero occupancy markers default status is 1 11 62 7 set draw hydrogens set draw hydrogens imol istat function Where e mol is an i
41. Copy chain from master to all related NCS chains Chapter 11 Scripting Functions 160 11 81 13 copy residue range from ncs master to others copy residue range from ncs master to others imol function master chain id residue range start residue range end Where e imolis an integer number e master chain id is a string e residue range start is an integer number e residue range end is an integer number Copy residue range to all related NCS chains If the target residues do not exist in the peer chains then create them 11 81 14 ncs control change ncs master to chain ncs control change ncs master to chain imol ichain function Where e imol is an integer number e ichain is an integer number change the NCS master chain by number 11 81 15 ncs control change ncs master to chain id ncs control change ncs master to chain id imol chain id function Where e imolis an integer number e chain d is a string change the NCS master chain by chain id 11 81 16 ncs control display chain ncs control display chain imol ichain state function Where e imolis an integer number e ichain is an integer number e state is an integer number display the NCS master chain 11 82 Helices and Strands Chapter 11 Scripting Functions 161 11 82 1 place helix here place helix here function add a helix Add a helix somewhere close to this point in the map try to fit the orientation Add to a molecule called Helix cre
42. Leuel 87 change model molecule representation mode ECCL tc A E 141 change residue number 117 check chiral volumes esses 122 Check dir and get url s 192 chiral center inverter sss 211 chiral centre inverter sess 211 cif file for comp id obe IARE 185 cis peptides gui s se 191 Clear all fized atoms 173 clear all viewS eee 133 clear and update model molecule from file acd estende euo shat LC MULA A DA T tte 76 clear and update molecule 181 Clear backup eui cece eee 186 Clear backups aavbe nno 186 clear ball and stick esses 141 Clear dos mil a ibi 143 clear dots by name 0 scene 143 Clear pending pilcke esee 108 click select residues for jligand 185 E ds oe Staal 203 ClLose generic obiect eee 171 closest aLtonm ccce ee EORR 182 EHS EE Netgen 186 command in path or absolute 203 command in path 203 211 212 control key for rotate state 80 COUTO ipse 187 coot has pygtk oiie cd dede tul di as 211 coot listener idle function proc 199 coot menubar menu sse 189 coot mkdir 1 20 22 df et es See E A 204 coot real exit ne e 71 coot replace string eee eee 202 coot socket timeout func 199 coot split version string 210 coot thread dispatcher sss 185 coot updates error handl
43. Restoring from Backup There may be certain circeumstances in which you wish to restore from a backup but can t get it by the Undo mechanism described above In that case start coot as normal and then open the typically most recent coordinates file in the directory coot backup or the directory pointed to the environment variable COOT_BACKUP_DIR if it was set This file should contain your most recent edits In such a case it is sensible for neatness purposes to immediately save the coordinates probably to the current directory so that you are not modifying a file in the backup directory See also Section Section 1 8 Crash page 4 3 12 View Matrix It is sometimes useful to use this to orient the view and export this orientation to other programs The orientation matrix of the view can be displayed in the console using view matrix Also the internal representation of the view can be returned and set using view quaternion to return a 4 element list set view quaternion i j k 1 which sets the view quaternion So the usage of these functions would be something like let v view quaternion manipulate v here maybe apply set view quaternion v or system manager 15 Tt works like the Forwards buttons in a web browser which is not available immediately after viewing a new page 16 for example if coot crashes Chapter 3 General Features 15 3 13 Space Group and Symmetry Occasionally you
44. Variance This idea is from Eleanor Dodson who liked to use the standard deviation of a residue s temperature factors to highlight regions of questionable structure Note that Hydrogens are ignored in this analysis 7 9 4 Peptide Omega Angle Distortion Some variability of the w is to be expected in the peptide bond But not too much Anything more than 13 degrees is suspicicous Unexpected peptide bonds show up red by default If cis peptides are to be expected and should not marked as bad then you can tell this to Coot using Edit gt Preferences gt Geometry gt Cis Peptides gt No Chapter 8 Representation 59 8 Representation 8 1 Surfaces Coot uses the surface code from Gruber and Noble 2004 Coot uses the partial charges of the atoms the partial_charge field in the chem comp atom block from the charge dictionary item in the refmac or other cif dictionary However partial charges are only used under certain conditions 1 the molecule consists of less than 100 atoms or 2 the number of atoms in the molecule that are hydrogens is at least 15 of the total number of atoms in the molecule If partial charges are not used then the fall back is to use charges from side chains charged at physiological pH Arg Lys Asp Glu Chapter 9 Hints and Usage Tips 9 Hints and Usage Tips 9 1 Documentation This manual is on the web where it can be searched e http www biop ox ac uk coot doc user manual html mon
45. a std string have sensible free_r_flag is an integer number make_molecules_ flag is an integer number refmac count string is a std string swap map colouwrs_post_refmac flag is an integer number imol_refmac_map is an integer number diff_map _flag is an integer number phase combine flag is an integer number phib_string is a std string fom_string is a std string ccp4i_project_dir is a std string if swap map colours post refmac flag is not 1 thenn imol_refmac_map is ignored 12 5 Dictionary Functions 12 5 1 dictionaries read dictionaries read function return a list of all the dictionaries read 12 6 Restraints Interface 12 6 1 set monomer restraints set monomer restraints monomer type restraints function Where e monomer type is a string restraints is a SCM set the monomer restraints of the given monomer type Returns scheme false or true for success or failure to set the restrains for monomer type 12 7 Atom Information functions Chapter 12 More Seripting Functions 181 12 7 1 residue info residue info imol chain_id resno ins_code function Where e mol is an integer number e chain id is a string e resno is an integer number e ins_code is a string Return a list of atom info for each atom in the specified residue output is like this list list list atom name alt conf list occ temp fact element list x y z 12 7 2 add molecule add molecule molecule_expression name f
46. active for other values of on or off turn on all models 11 38 10 show spacegroup show spacegroup imol function Where mol is an integer number return the spacegroup of molecule number imol Deprecated Returns No Spacegroup when the spacegroup of a molecule has not been set 11 39 Align and Mutate 11 39 1 align and mutate align and mutate imol chain_id fasta maybe renumber residues flag function Where e imolis an integer number e chain id is a string e fasta maybe is a string e renumber residues flag is an integer number aligand and mutate the given chain to the given sequence 11 39 2 set alignment gap and space penalty set alignment gap and space penalty wgap wspace function Where e wgap is a number e wspace is a number set the penalty for affine gap and space when aligning defaults 3 0 and 0 4 Chapter 11 Scripting Functions 117 11 39 3 align to closest chain align to closest chain target_seq match fraction function Where e target_seq is a string e match_fraction is a number align sequence to closest chain compare across all chains in all molecules Typically match_fraction is 0 95 or so Return 1 if we were successful 0 if not 11 40 Renumber Residue Range 11 40 1 renumber residue range renumber residue range imol chain_id start res last re offset function Where e imolis an integer number e chain_id is a string e start_res is an integer number e Jost res i
47. altconf is a string refine a zone using auto range presumes that imol_Refinement_Map has been set 11 43 18 regularize zone regularize zone imol chain_id resnol resno2 altconf Where e mol is an integer number e chain id is a string e resnol is an integer number e resno is an integer number e altconf is a string regularize a zone 121 function function function function Returns a status whether the regularisation was done or not 0 for no 1 for yes Chapter 11 Scripting Functions 122 11 43 19 set dragged refinement steps per frame set dragged refinement steps per frame v function Where v is an integer number set the number of refinement steps applied to the intermediate atoms each frame of graphics smaller numbers make the movement of the intermediate atoms slower smoother more elegant Default 80 11 43 20 dragged refinement steps per frame dragged refinement steps per frame function return the number of steps per frame in dragged refinement 11 43 21 set refinement refine per frame set refinement refine per frame istate function Where istate is an integer number allow refinement of intermediate atoms after dragging before displaying default 0 off An attempt to do something like xfit does at the request of Frank von Delft Pass with istate 1 to enable this option 11 43 22 refinement refine per frame state refinement refine per frame state function query the
48. and map molecules combined that are currently in coot Returns the number of molecules closed molecules are not counted 11 8 9 toggle idle spin function toggle idle spin function function Spin spin spin or not 11 8 10 toggle idle rock function toggle idle rock function function Rock not roll self timed 11 8 11 set rocking factors set rocking factors width scale frequency scale function Where e width scale is a number e frequency scale is a number Settings for the inevitable discontents who dislike the default rocking rates defaults 1 and 1 11 8 12 set idle function rotate angle set idle function rotate angle f function Where f is number how far should we rotate when auto spinning Fast computer set this to 0 1 11 8 13 handle read draw molecule handle read draw molecule filename function Where filename is a string a synonym for read pdb Read the coordinates from filename can be pdb cif or shelx format 11 8 14 set convert to v2 atom names set convert to v2 atom names state function Where state is an integer number shall we convert nucleotides to match the dictionary names Usually we do not want to do this give current Coot architecture Most often not though Coot should handle the residue synonyms transparently default off 0 Chapter 11 Scripting Functions 11 8 15 handle read draw molecule with recentre handle read draw molecule with recentre filename fu
49. apply ncs to view orientation and screen CERT Oaea A er UE 78 assien fasta seduence 165 assign hetatms 6 cece eee eens 74 assign pir sequence eee 165 assign sequence from file 165 assign sequence from string 165 assoclate pir Zile 208 associate pir with molecule gui 191 atom spec to atom index s 113 atom specs wed outa hee etnies 207 auto Zit best rotaner eee eee 148 auto fit rotamer active residue 196 auto read do difference map too state 91 auto read make and draw maps 91 auto weight for refinement 207 B background demo 212 background is black p ssssssssresno 134 backup compress files state 83 back p state o d AE AE ete tous 82 BAEL AND STICK see ons Sg Bat eee 209 baton build delete last residue 152 baton try another esee 152 blob under pointer to screen centre 80 brief atom labels state 131 bright Map ici maur e Ed Rep 206 brighten Maps coru maf epa put ut war 206 br wSer rlc si ld ed 167 C cache or net get image s ss 185 cached pisa analysis sess 200 calc phases generic sess 83 Function Index center atom label status 198 CONTEO MAS ii EEN 198 ee 207 chain Xds i eR IRE ba a 206 chain n residues e i e es 67 Change contour
50. bumps 126 set show environment distances h bonds 126 set show graphics ligand view 178 set show origin marker 78 set show paths in display manager 65 set show pointer distances 127 set show strict ncS eee 159 set show symmetry master 96 set show symmetry molecule 96 set show unit cell sees 102 set show unit cells all 102 Set Skeleton bos size sss 110 set smooth scroll do zoom 127 Set Smootbh scroll flag 107 set smooth scroll limit 107 set smooth scroll steps 107 set solid density surface opacity 76 set Space Qroup E 100 Set Sticku sort b date sss 66 set stop scroll diff map 88 set stop scroll diff map level 88 set stop scroll iso map sess 88 set stop scroll iso map level 88 set swap difference map colors 198 set swap difference map colours 92 set symmetry colour eese 103 set symmetry molecule rotate colour map 97 set symmetry shift search size 100 set symmetry size eee 96 set transparent electrostatic surface 166 set undo molecule cc cece cece ees 82 set unpathed backup file names 83 Set vileumattiz 0 0 eee 187 205 set view quaternion eee 78 set virtual tr
51. chooser stub state ooooocooommm 151 11 72 Pointer Atom Functions 0 0 ccc eee eee eee eee 151 11 72 1 create pointer atom molecule maybe 151 11 72 2 pointer atom molecule 0 00 cece eee oc 151 11 73 Baton Build Interface Functions 0000200 151 11 73 1 set baton mode eee 151 11 73 2 Tre set draw baton 0 00 ccc eee eee ees 151 11 73 3 accept baton position 0 00 e cece eee eee 152 11 73 4 baton rv anotbher 0 0 0 152 11 73 85 shorten baton 0 0 cece eee e 152 11 73 6 lengthen baton 0 cece eee eee eee 152 11 73 7 baton build delete last residue eee eee 152 11 73 8 set baton build params esee 152 11 74 Crosshairs Interface 152 11 74 1 set draw crosshairs sees 152 11 75 Edi Chi Amoles euer ge eier e 152 11 75 1 set find hydrogen torsions sees 153 11 75 2 edit chi angles sese 153 11 75 3 oetup toraion general eee 153 TAG Mask is at oe Sates ipe reden Qa e MUN e CIE 153 11 76 1 mask map by molecule 0 cc eee eee eee 153 11 76 2 set map mask atom radius 0 e cece eee 153 11 76 38 map mask atom radius 0 cece eee ee eee 154 11 77 check Waters Interface 154 11 77 1 delete checked waters baddies 000s eee 154 DDB DEB epe iui er e eer oft ire rob rero deti teu 154 11 78 1 trim molecule by Map o 154 11 79 External Ray Tracing 0 ccc eee eens 154 xviii
52. code is a string e representation_type is an integer number e bonds boz type is an integer number e bond width is a number e draw hydrogens flag is an integer number return the index of the additional representation Returns 1 on error 11 63 Dots Representation 11 63 1 dots dots imol atom selection str dots_object_name dot density function sphere size scale Where e imolis an integer number e atom selection str is a string e dots object name is a string e dot density is a number e sphere_size_scale is a number display dotted surface return a generic objects handle which can be used to remove later 11 63 2 set dots colour set dots colour imolrgb function Where e imolis an integer number e risa number e gisa number e bisa number set the colour of the surface dots of the imol th molecule to be the given single colour r g b are values between 0 0 and 1 0 11 63 3 unset dots colour unset dots colour imol function Where mol is an integer number no longer set the dots of molecule imol to a single colour i e go back to element based colours Chapter 11 Scripting Functions 11 63 4 clear dots clear dots imol dots handle Where e imol is an integer number e dots handle is an integer number clear dots in imol with dots handle 11 63 5 clear dots by name clear dots by name imol dots_object_name Where e imol is an integer number e dots object name is a string clear the
53. colours colour flag pass 1 for on 0 for off colour index 0 to 7 inclusive for various different colourings 11 23 State Functions 11 23 1 save state save state function save the current state to the default filename 11 23 2 save state file save state file filename function Where filename is a string save the current state to file filename 11 23 3 set save state file name set save state file name filename function Where filename is a string set the default state file name default 0 coot state scm 11 23 4 set run state file status set run state file status istat function Where istat is an integer number set run state file status 0 never run it 1 ask to run it 2 run it no questions 11 23 5 run state file run state file function run the state file reading from default filenname 11 23 6 run state file maybe run state file maybe function run the state file depending on the state variables Chapter 11 Scripting Functions 11 24 Unit Cell interface 11 24 1 get show unit cell get show unit cell imol Where mol is an integer number return the stage of show unit cell for molecule number imol 11 24 2 set show unit cells all set show unit cells all istate Where state is an integer number set the state of show unit cell for all molecules 1 for displayed 0 for undisplayed 11 24 3 set show unit cell set show unit cell imol istate Where e imol is an integer number e stat
54. dialog Section Section 3 11 Backups and Undo page 13 5 7 2 Missing Skeleton Sometimes especially at loops you can see the direction in which the chain should go but there is no skeleton see Section Section 6 14 Skeletonization page 52 is displayed and consequently no guide points in that direction In that case Undo the previous atom and decrease the skeletonization level Edit gt Skeleton Parameters gt Skeletonization Level Accept the atom in the same place as last time and now when the new guide points are displayed there should be an option to build in a new direction 5 7 3 Building Backwards The following scenario is not uncommon you find a nice stretch of density and start baton building in it After a while you come to a point where you stop dismissing the baton build dialog You want to go back to where you started and build the other way How do you do that e Use the command set baton build params start resno chain id backwards where start resno would typically be 0 and chain id would be default e Recentre the graphics window on the first atom of the just build fragment e Select Ca Baton Mode and select a baton direction that goes in the opposite direction to what is typically residue 2 This is slightly awkward because the initial II y again toggles the mode off 12 high resolution map interpretation is planned 13 ie one less than the starting residue in the for
55. did not work Chapter 11 Scripting Functions 174 11 98 CCP4mg Interface 11 98 1 write ccp4mg picture description write ccp4mg picture description filename function Where filename is a string write a ccp4mg picture description file 11 98 2 get atom colour from mol no get atom colour from mol no imol element function Where e mol is an integer number e element is a string get element colour for imol as Python formatted list char 11 99 Aux functions 11 99 1 laplacian laplacian imol function Where mol is an integer number Create the Laplacian ve second derivative of the given map 11 100 SMILES 11 100 1 do smiles gui do smiles gui function display the SMILES string dialog 11 101 PHENIX Support 11 101 1 set button label for external refinement set button label for external refinement button label function Where button label is a string set the button label of the external Refinement program 11 102 Graphics Text 11 102 1 place text place text text x y z size function Where e text is a string Chapter 11 Scripting Functions 175 e x is a number e y is a number e zis a number e size is an integer number Put text at x y z size variable is currently ignored Returns a text handle 11 102 2 remove text remove text text_handle function Where text_handle is an integer number Remove 3d text item 11 102 3 text index near position text index near position xy
56. e bis a number e cisa number e alpha is a number e beta is a number e gamma is a number read phs file use coords to use cell and symm to make map in degrees Chapter 11 Scripting Functions 11 35 5 read phs and make map with reso limits read phs and make map with reso limits imol phs_file_name reso_lim_low reso lim high Where e imolis an integer number e phs file name is a string e reso lim low is a number e reso lim high is a number 112 function read a phs file and use the cell and symm in molecule number imol and use the resolution limits reso lim high in Angstroems 11 36 Graphics Move 11 36 1 undo last move undo last move undo last move 11 36 2 translate molecule by translate molecule by imol x yz Where e mol is an integer number e zx is a number e y is a number e zis a number translate molecule number imol by x y z in Angstroms 11 36 3 transform molecule by transform molecule by imol m11 m12 m13 m21 m22 m23 m31 m32 m33 XyZ Where e imol is an integer number e mii is a number e m 2 is a number e m13 is a number e m21 is a number e m22 is a number e m23 is a number e m31 is a number e m32 is a number function function function Chapter 11 Scripting Functions 113 e m33 is a number e risa number e y is a number e z isa number transform molecule number imol by the given rotation matrix then translate by x y z in Angstroms 11 37 Go To Atom W
57. e end_resno is an integer number delete residue range 11 67 2 delete residue delete residue imol chain id resno inscode Where e imolis an integer number e chain_id is a string e resno is an integer number e inscode is a string delete residue 145 function function function function function Chapter 11 Scripting Functions 11 67 3 delete residue with full spec delete residue with full spec imol imodel chain_id resno inscode altloc Where e mol is an integer number e model is an integer number e chain_id is a string e resno is an integer number e inscode is a string e altloc is a string delete residue with altconf 11 67 4 delete residue hydrogens delete residue hydrogens imol chain id resno inscode altloc Where e imolis an integer number e chain_id is a string e resno is an integer number e inscode is a string e altloc is a string delete hydrogen atoms in residue 11 67 5 delete atom delete atom imol chain id resno ins code at name altloc Where e imolis an integer number e chain_id is a string e resno is an integer number e ins code is a string e ai name is a string e altloc is a string delete atom in residue 11 67 6 delete residue sidechain delete residue sidechain mol chain id resno ins code do delete dialog Where e imol is an integer number e chain id is a string 146 function function function function Chapter 11 Scr
58. eee eens 117 11 41 Scripting Interface 117 11 41 1 probe available p 00 o 117 11 41 2 pDost acnpting windom 0 00 cece eee eee eee 118 11 41 38 post scheme scripting window 2 eee ee ee 118 11 41 4 post python scripting window 000e eee 118 11 42 Monomer veia ee teed RD eet ae EN 118 11 42 1 get coords for accession code cece eee ee eee 118 11 42 2 get monomer 0 ce eee eee nn 118 11 42 3 TUNES CTI Pinta kee Loa dae Meee wei eee RS 118 11 43 Regularization and Refinement 00 eee eee 118 11 43 1 add polanar peptide restraints cece ee eee 118 11 43 2 remove planar peptide restraints ooooooccccooom 119 11 43 3 addomega toraion restriants ss ssrrsrses 119 11 43 4 remove Oomega Lorsion restriante 119 11 43 5 set refinement immediate replacement 119 11 43 6 refinement immediate replacement state 119 11 43 7 set residue selection flash frames number 119 11 43 8 accept regularizement sess 119 11 43 9 set zebne a th Aoron restraimnto esses 120 11 43 10 refine with torsion restraints state sess 120 11 49 1T1 esetematrix ii C SUE 120 11 43 12 matrix staten L dae ep eER Mee e 120 11 43 13 set refine auto range step 0 20 0c cece eee eee eee 120 11 43 14 oet rebne mas reaidues 0 c cece ence e ees 120 11 43 15 refine zone atom index define 200 000 121 IL43 16 TOMEN cc Gy tei de
59. elt tle ue 213 Concept Index aci ri eee eels 215 Function Index sese 218 Chapter 1 Introduction 1 1 Introduction This document is the Coot User Manual giving an overview of the interactive features Other documentation includes the Coot Reference Manual and the Coot Tutorial These documents should be distributed with the source code 1 1 Citing Coot and Friends If have found this software to be useful you are requested if appropriate to cite Features and Development of Coot P Emsley B Lohkamp W Scott and K Cowtan Acta Cryst 2010 D66 486 501 Acta Crystallographica Section D Biological Crystallography 66 486 501 The reference for the REFMAC5 Dictionary is REFMAC5 dictionary Organization of Prior Chemical Knowledge and Guide lines for its Use Vagin AA Steiner RA Lebedev AA Potterton L McNicholas S Long F Murshudov GN Acta Crystallographica Section D Biological Crystal lography 60 2184 2195 Part 12 Sp Iss 1 DEC 2004 If using SSM Superposition please cite Secondary structure matching SSM a new tool for fast protein structure alignment in three dimensions Krissinel E Henrick K Acta Crystallographica Section D Biological Crystallography 60 2256 2268 Part 12 Sp Iss 1 DEC 2004 The reference for the the Electron Density Server is GJ Kleywegt MR Harris JY Zou TC Taylor A W hlby TA Jones 2004 The Uppsala Electron Density Server Acta Crystallographica Se
60. from ncs master to others imol master chain id start resno end resno e g copy residue range from ncs master to others O A 1 5 If you want to copy a residue range to a specific chain or specific list of chains rather than all NCS peer chains then make a list of the chain ids that you wish replaced copy residue range from ncs master to chains O A 15 list C in this case just the residues in the C chain is replaced 5 31 Running Refmac Use the Run Refmac button to select the dataset and the coordinates on which you would like to run Refmac Note that here Coot only allows the use of datasets which has Refmac parameters set as the M TZ file was read By default Coot displays the new coordinates and the new map generated from refmac s output MTZ file Optionally you can also display the difference map You can add extra parameters data lines to refmac s input by storing them in a file called refmac extra params in the directory in which you started coot You can also provide extra replacement parameters for refmac by setting the variable refmac extra params to a list of strings for example set refmac extra params list REFINE MATRIX 0 1 MAKE HYDROGENS NO Coot blocks 5 until Refmac has terminated The default refmac executable is refmac5 it is presumed to be in the path If you don t want this it can be overridden using a re definition either at the scripting interface or in one s coot file e g
61. geometry restraints for refmac and use them in fragment zone ide alization this is called Regularization The geometrical restraints are by default bonds angles planes and non bonded contacts You can additionally use torsion re straints by Calculate gt Model Fit Refine Refine Regularize Control gt Use Torsion Restraints Truth to tell this has not been successful in my hands sadly RS Real Space Refinement after Diamond 1971 in Coot is the use of the map in addition to geometry terms to improve the positions of the atoms Select Regularize from the Model Fit Refine dialog and click on 2 atoms to define the zone you can of course click on the same atom twice if you only want to regularize one residue Coot then regularizes the residue range At the end Coot displays the intermediate atoms in white and also displays a dialog in which you can accept or reject this regularization In the console are displayed the x values of the various geometrical restraints for the zone before and after the regularization Usually the x values are considerably decreased structure idealization such as this should drive the x values toward zero The use of Refinement is similar with the addition of using a map The map used to refine the structure is set by using the Refine Regularize Control dialog If you have read created only one map into Coot then that map will be used there is no need to set it explici
62. index of the new restraint Returns 1 when the atoms were not found and no extra bond restraint was stored 11 43 33 delete all extra restraints delete all extra restraints imol function Where mol is an integer number clear out all the extra user defined restraints for molecule number imol 11 43 34 delete extra restraints for residue delete extra restraints for residue imol chain id res no ins code function Where e imolis an integer number e chain d is a string e res no is an integer number e ins_code is a string clear out all the extra user defined restraints for this residue in molecule number imol Chapter 11 Scripting Functions 11 44 Simplex Refinement Interface 11 44 1 fit residue range to map by simplex fit residue range to map by simplex resl res2 altloc chain_id mol imol for map Where e resi is an integer number e res2 is an integer number e altloc is a string e chain d is a string e imolis an integer number e imol for map is an integer number refine residue range using simplex optimization 11 44 2 score residue range fit to map score residue range fit to map resl res2 altloc chain_id imol imol_for_map Where e resi is an integer number e res2 is an integer number e altloc is a string e chain d is a string e imol is an integer number e imol_for map is an integer number simply score the residue range fit to map 11 45 Nomenclature Errors 11 45 1 fix nomenclature errors fix nomenclatu
63. label is f don t make one otherwise create with with the given label and on state cache or net get image image url image name func procedure Get image name caller doesn t care how and when it is in place run func This is a generally useful function so it has been promoted outside of dig table refmac calc sfs make mtz pdb in file name mtz file name procedure mtz refmaced file name return refmac result or f pdbe get pdb and sfs cif include get sfs flag entry id procedure Use progress bars include get sfs flag is either no sfs or include sfs pdbe latest releases gui procedure Sameer Velankar says to get this file for the latest releases http www ebi ac uk pdbe apps jsonizer latest released note the end Chapter 13 Scheme Scripting Functions 186 13 4 jligand to jligand secret file namex procedure JLigand sends Coot a file that contains filenames for the link and new dictionary restraints jligand home env procedure Define an environment variable for the place where jligand jar resides in a canonical distribution imol jligand link procedure jligand internal parameter get file mtime file name procedure this could be in utils start jligand listener procedure every fraction of a second look to see if from jligand secret link file name has been updated If so then run the handle read from jligand file function 13 5 user define restraints run prosmart imol target
64. masked by a set of coordinates Use the scripting function mask map by molecule imol map imol model invert mask If invert mask is 0 this will create a new map that has density only where there are no close coordinates If invert mask is 1 then the map density values will be set to zero everywhere except close to the atoms of molecule number mol model The radius of the mask around each atom is 2 0 by default You can change this using 8 If you re living in Sweden or Captain Kirk that is 3 you may think it strange that a box has a radius this is an idiosyncrasy of Coot Chapter 6 Map Related Features 53 set map mask atom radius radius There is a GUI interface to Map Masking under the Extensions menu 6 17 1 Example If one wanted to show just the density around a ligand 1 Make a pdb file the contains just the ligand and read it in to Coot let s say it is molecule 1 and the ligand is residue 3 of chain L 2 Get a map that covers the ligand e g from refmac Let s say this map is molecule number 2 3 Mask the map mask map by molecule 2 1 1 This creates a new map Turn the other maps off leaving only the masked map To get a nice rendered image press F8 see Section Section 3 6 Raster3D page 10 6 18 Trimming If you want to remove all the atoms that lie outside the map i e in low density you can use trim molecule by map imol coords imol map density level delete zero occ wher
65. model modifications are automatically applied 13 15 refmac problems refmac problems gui imol problem list procedure The gui for the refmac problems 13 16 get ebi check dir and get url procedure check the directory and get url url string get url str procedure get url string for data type pdb or sfs get ebi pdb id procedure Return a molecule number on success or not a number f or 1 on error Chapter 13 Scheme Scripting Functions 193 13 17 brute lsqman lsqman count procedure brute lsqman run lsqman on chains A of two pdb files and read in the result to coot Charlie Bond 2003 Can keep a count of the number of successful runs if necessary 13 18 entry do button teb procedure test that function teb2 procedure test that function 13 19 prodrg import prodrg xyzin procedure if there is a prodrg xyzin set the current time to its mtime else f import from 3d generator from mdl mdl file name procedure This function can be overwritten by your favourite 3d conformer and restraints gen erator get mdl latest time procedure not needed prodrg flat imol in chain id in res no in procedure return f if fail or a list of the molecule number of the selected residue the prodrg output mol file name the prodrg output pdb file name get sbase monomer and overlay comp id procedure import from SBASE callback using sbase import function 13 20 fascinating things fascinating cluster
66. molecule number imol do a rigid body fit of the water to the density stepped refine protein imol res step procedure Step through the residues of molecule number imol and at each step do a residue range refinement unlike fit protein for example which does real space refinement for every residue The step is set internally to 2 stepped refine protein for rama imol procedure refine each residue with ramachandran restraints stepped refine protein with refine func imol refine func procedure res step post ligand fit gui procedure The GUI that you see after ligand finding molecules matching criteria test func procedure test func is a function given one argument a molecule number that returns either HH if the condition is not satisfied or something else if it is And that something else can be a list like list label x y z or list Bad Chiral 0 A 23 CA A It is used in the create a button label and what to do when the button is pressed Chapter 13 Scheme Scripting Functions 196 refine active residue generic side residue offset procedure This totally ignores insertion codes A clever algorithm would need a re write I think Well we d have at this end a function that took a chain id res no 1 ins code 1 res no 2 ins code 2 And refine zone would need to be re written too of course So let s save that for a rainy day days weeks refine active residue procedure refine active residue refine a
67. move just one atom In more up to date versions Coot will display colour patches something like a traffic light system representing the chi squared values of each of types of geometric feature refined Typically 5 greens is the thing to aim for the colour changes occurring at chi squared values 2 5 and 8 8 being the most red To prevent the unintentional refinement of a large number of residues there is a heuristic fencepost of 20 residues A selection of than 20 residues will not be regularized or refined The limit can be changed using the scripting function e g set refine max residues 30 5 1 1 Dictionary The geometry description for residues monomers and links used by Coot are in the standard mmCIF format Because this format alows multiple comp ids residue types to be described within a cif loop it is hard to tell when a dictionary entry needs to be overwritten when reading a new file Therefore Coot makes this extra constraint that the chem comp loop should appear first in the comp list data item if this is the case then Coot can overwrite an old restraint table for a particular comp id residue type when a new one is read By default the geometry dictionary entries for only the standard residues are read in at the start It may be that your particular ligand is not amongst these To interactively add a dictionary entry use File Import CIF Dictionary Alternatively you can use the function rea
68. n atomS sese eee 75 hetify residue tii io 74 hide main toolbar see 79 hide modelling toolbar 79 hilight binding site 005 210 hole shea apis da eed 184 I ideal nucleic acid 0 cece 163 identity matriz iii ceed Sas a 205 imol refinement map sees 123 import from 3d generator from mdl 193 221 increment coot tip number 212 info dialog iuvene 67 info dialog and t xt ecos ri rirse odi tanirini xi 67 insert action view after view 133 insertion code from serial number 68 interactive probe Vitali dd po 194 interactive probe dots molprobity radius Suto ce e dbi Oe NN 172 Jnteresting Chinge geui sss 188 interesting things with fix maybe 188 interruptible fit protein 195 is closed generic object p 171 is closed generic object 194 is difference map iii nce ieee erii 207 A ccu le I Te 204 is solvent chain p eee es 68 is solyent chain miii 206 J jiggl ed molg bie r i 198 K keep map colour after refmac state 95 L label all active residue atoms 209 label all atoms in residue 209 label all CAS oues N 209 laplacran s i ive ete ket oboe ee bbs bey hbo 174 launch jligand function 185 Lengtben barton 6 cece cece 152 ENEE ead eI 193 ligand expert i e vb EE 135 ligand s
69. nieee rrasa eona p Ea e eee 46 moving molecules 46 Moving Zero Occupancy Atoms 30 multi mutate s ereere entere use eee eee eee eens 37 multiple coordinates fileS ooooo 18 MUG ALC ssa awe neret ku rrr eei Vp E baleen EE 3T mutatins DNA ore i Eae rv 37 mu tating RNA ote taa ias 37 N NOS tin an iaa 20 NCS averaging cese 21 NES edits sora iki mr ens 43 negative contour levels ssusuusuurr rnn 50 216 O QQ A erates paa 21 OpenGL Eed ER a We de bie hi de 9 Orientation Axen 16 ricin marker 22 vLbperte ek 639i Qe ewes 9 OUtpUt ENEE EE eee keke ewe A dg dem 17 overlaying ligands 0 00004 25 OXT atom Lev rita 41 P packing diagram cece eee eee ee eee 22 Patterson dubii praia 52 IO 36 peptide restraints planar 29 PHS d ta ara NE ee eee 49 PHS data format eeepc 48 O Dn ca eae os 61 pink pointer cesta lias wees aida 16 planar peptide restraints essssrsrsrenu 29 planes dedii pP hue reg to 27 polynucleotides sneuesususueneerneen rnn 42 post manipulation ho0k oooooocccconmmc 31 Print Sequence cece cece eee eens 23 PIODE vespa woe eae E ANE 57 python si levi Sih Shae A tras 12 R Ramachandran plot 55 Raster3D 3 d o at EEN ENER e taa de 10 reading multiple pdb fileS o o 18 recentring ale se cae Lie it n err 15 recover Session 4 LOU tay o AVE Msn ueber de 14 red cesscssiee ga EEN ENNEN a
70. radius of the screen centre Return nothing interesting Chapter 13 Scheme Scripting Functions 195 13 23 fitting fit protein imol procedure Note that residue with alt confs do not undergo auto fit rotamer This is because that autofit rotamer then refine will tend to put both rotamers into the same place Not good It seems a reasonable expectation that residues with an alternate conformation are already resonably well fitted So residues with alternate conformations undergo only real space refinement This is simple minded and outdated now we have the interruptible version below continue multi refinex procedure These 2 variables are used by multi refine function s called by idle functions to refine just one residue fit protein make specs imol chain specifier procedure chain specifier can be a string where it is the chain of interest or all chains where all chains are chosen interruptible fit protein mol func procedure func is a refinement function that takes 2 args one a residue spec the other the imol refinement map e g fit protein fit function fit chain imol chain id procedure For each residue in chain chain id of molecule number imol do a rotamer fit and real space refinement of each residue Don t update the graphics while this is happening which makes it faster than fit protein but much less interesting to look at fit waters imol animate procedure For each residue in the solvent chains of
71. refine residues A501 and A503 and residue A502 if it exists will be an anchoring residue used in optimizing the link geometry of the atoms in A501 and A503 5 1 4 Refining Carbohydrates Refining carbohydrates monomers should be as straightforward as refining a protein residue Coot will look in the dictionary for the 3 letter code for the particular residue type if it does not find it Coot will try to search for dictionary files using b D or a L extensions When refining a group of carbohydrates the situation needs a bit more explanation For each residue pair with tandem residue numbers specified in the refinement range selection Coot checks if these residue types are are furanose or pyranose in the dictionary and if the are both one or the other then it tries to see if there are any of the 11 link types BETA1 4 BETA2 3 ALPHA1 2 and so on specified in the dictionary It does this by a distance check of the potentially bonding atoms If the distance is less than 3 0A then a glycosidic bond is made and used in the refinement Bonds between protein and carbohydrate and branched carbohydrates can be refined using Sphere Refinement Instead of using a sphere to make a residue selection you can specify the residues directly using refine residues for example refine residues 0 L 501 L 503 LINK and LINKR cards are not yet used to determine the geometry of the restraints 5 1 5 Planar Peptide Rest
72. res no is an integer number e ins code is a string e res type is a string mutate a base return success status 1 for a good mutate 11 71 4 set mutate auto fit do post refine set mutate auto fit do post refine istate function Where istate is an integer number Do you want Coot to automatically run a refinement after every mutate and autofit 1 for yes 0 for no 11 71 5 mutate auto fit do post refine state mutate auto fit do post refine state function what is the value of the previous flag 11 71 6 set rotamer auto fit do post refine set rotamer auto fit do post refine istate function Where istate is an integer number Do you want Coot to automatically run a refinement after every rotamer autofit 1 for yes 0 for no 11 71 7 rotamer auto fit do post refine state rotamer auto fit do post refine state function what is the value of the previous flag 11 71 8 mutate single residue by serial number mutate single residue by serial number ires ser chain_id imol function target res type Where e ires_ser is an integer number e chain id is a string Chapter 11 Scripting Functions 151 e mol is an integer number e target_res_type is a character an alternate interface to mutation of a singe residue ires ser is the serial number of the residue not the seqnum There 2 functions don t make backups but does CHECKME Hence is for use as a one by one type and the following 2 by wrappers that muate either
73. residues of your protein could well have the correct se quence but be chopped back to CG or CB atoms There is a function to fill such partially filled residues fill partial residues imol This identifies residues with missing atoms then fills them and does a rotamer fit and real space refinement If you want to fill the side chain of just one residue fill partial residue imol chain id res no ins code this does a auto fit best rotamer and a refinement on the resulting side chain position 5 38 Changing Chain IDs You can change the chain ids of chains using Calculate gt Change Chain IDs Coot will block an attempt to change the whole of a chain and the target chain id already exists in the molecule If you use the Residue Range option then you can insert residues with non conflicting residue number into pre existing chains 41 the current single function doesn t always perform very well in tests 42 suspect that there is not one tool that fits for all Chapter 5 Modelling and Building 5 39 Setting Occupancies As well as the editing Residue Info to change occupancies of individual atoms one can use a scripting function to change occupancies of a whole residue range e zero occupancy residue range imol chain id resno start resno last example usage zero occupancy residue range 0 A 23 28 This is often useful to zero out a questionable loop before submitting for refinement After refinement with refm
74. second atom that you click will be the local rotation centre for the zone The atoms selected in the moving fragment have the same alternate conformation code as the first atom you click To actuate a transformation click and drag horizontally across the relevant button in the newly created Rotation amp Transla tion dialog The axis system of the rotations and translations are the screen coordinates Alternatively you can click using left mouse on an atom in the fragment and drag the fragment around Use Control Left mouse to move just one atom rather than the whole fragment If you click Control Left mouse whilst not over an atom then you can rotate the fragment using mouse drag Click OK or press Return when the transformation is complete To change the rotation point to the centre of the intermediate atoms rather than the second clicked atom use the setting set rotate translate zone rotates about zone centre 1 5 4 Rigid Body Refinement Rigid Body Fit Zone from the Model Fit Refine dialog provides rigid body refinement The selection is zone based So to refine just one residue click on one atom twice Sometimes no results are displayed after Rigid Body Fit Zone This is because the final model positions had too many final atom positions in negative density If you want to over rule the default fraction of atoms in the zone that have an acceptable fit 0 75 to be say 0 25 set rigid body fit acceptable fit f
75. sidechains eiue ser EDD ts E RV IERI 33 simplex refinement cece eee eee eee 31 single click reine 27 skeleton updating cesses 52 skeleton missing sscsucrrererrerrrrrrre 32 Sskeletonization esee 52 Slabs nr hie ots bebe ble EI ebbe E 16 SHIN Ser AR RTI EROR tr Pt 15 slow compluler scesiswese kv nd 62 SMILES strings er I5 rA e xe DON neu 38 space group Damen 18 space group operators sss eese 15 sphere refinement 0 e eee eee eee 28 startup dialog state 008 13 startup settings python esses 12 startup settings scheme lesse 12 Stabe drepe I SERO Ur ASI M 12 superposition sseeeeee ee 24 Symtetry e e deed d TREES 22 symmetry operators sss 15 T terminal oxygen cece eee eee ere 41 217 terminal residue cece eee eee ee oo 41 thickness of density Ines 50 tooltips citas il 8 torsion angles ligand s ssusrrerrrrreruo 36 torsion general pec Xep er Ta Sad 36 torsion retrait 27 COTTON EE 35 trackball virtuale ieu sane baaa 6 trafic lights iris RG Ae 28 translate molecule 0 cece eee eee eee 47 translation keyboard ooocococccccccccccc 6 translation mouse 00oocococcoococccoco ccoo 5 trimming atoms iie dax ru rere RES 53 U UNO ii ts 13 unexplained density 00 000005 56 unit clase Ic 16 UNK residue oo eagle dese eae ee be 30 unmodelled density
76. space group So allow the user to set it This can be initted with a HM symbol or a symm list for clipper Return the succes status of the setting 11 21 18 set symmetry shift search size set symmetry shift search size shift function Where shift is an integer number set the cell shift search size for symmetry searching When the coordinates for one or some symmetry operator are missing which hap pens sometimes but rarely try changing setting this to 2 default is 1 It slows symmetry searching which is why it is not set to 2 by default 11 22 History Functions 11 22 1 print all history in scheme print all history in scheme function print the history in scheme format 11 22 2 print all history in python print all history in python function print the history in python format 11 22 3 set console display commands state set console display commands state istate function Where istate is an integer number set a flag to show the text command equivalent of gui commands in the console as they happen 1 for on 0 for off 11 22 4 set console display commands hilights set console display commands hilights bold flag colour flag function colour index Where e bold_flag is an integer number Chapter 11 Scripting Functions 101 e colour flag is an integer number e colour Ander is an integer number set a flag to show the text command equivalent of gui commands in the console as they happen in bold and
77. string with no spaces else return f strip leading spaces str procedure 53 Zb wow gt n string append with string str ls tag str procedure Append strings with tag str between them strip extension s procedure a b res gt a b file name sans extension file name extension procedure What is the extension of file name a pdb gt pdb nn _ gt n add tmp extension to procedure e g a pdb a tmp pdb Chapter 13 Scheme Scripting Functions 204 file name sans extension procedure Same function as strip extension different name as per scsh in fact strip path s procedure a b t gt b t d e ext gt e ext file name sans path slash start s procedure does s start with a return t or f string concatenate ls procedure simple scheme functions to concat the strings in ls Is must contain only strings unique date time str procedure return a string that contains the date time e g 2006 01 02 2216 03 every nth lsn procedure return a list that has only every nth members e g every nth 0 1234567 8 2 gt 0 2368 every nth 012345678 3 gt 03 6 n must be positive get atom imol chain id resno ins code atom name alt conf procedure Return an atom info or f if atom not found multi read pdb glob pattern dir procedure multi read pdb reads all the files matching g1ob pattern in directory dir Typical usage of this might be multi read pdb a pdb
78. the Refinement Map 30 Chi angles S 8 ebd lee nee 35 Cif dicho Aia di eet A ir Web BRS et de 28 CHING COOL cs DEG CIE ari 1 clashing residues osucsucrecrecrerrrrrre 35 Clear Pending Dicks 44 clearing backups 00 0 0 cece eee 61 clippings sie yi ed sais HG ee Se ee See S 16 colour by chan 10 colouring atoms 0 eene 19 colouring map 50 command line arguments 00 3 215 Contouring Map 2 ses seeds Heese aes Sel 6 49 coordinates Tomat 18 coot droppings 2 cece ccoo eee eee eee ee 60 CLASH chp A SA eae ee 4 erash r coverya cuc RS 4 ee 2 Ra e Tk RIP DR ae es 16 D deb gger cc eire emm ERI RIDE te eae 4 default refmac executable ssrsucrrrcreuu 43 delete ciuium ai 44 density line thickness 005 50 d pth Cuein ge wees Psd hah tan PEERS 9 dictionary loci 2 39 dictionary ligands 00 0 000 3 difference map 49 51 difference map colourg eee eee eee 49 directory for save coordinates c ccus 11 Display Manager 10 DNA 1de l iin hicided sack SERA cosa ass 42 DNA mutating rv Ae d 37 docking sidechains 0 0200005 33 ele xis Meld tada 60 dual conformations esses 36 E edit chi angles 0 022 eee 35 edit B factors MEN A NEE E Ae dE A dE 19 edit OCCUPANCY e tera al 19 Electron Density Server ss susrirrrrnu 21 executing Commandes
79. the molecule that now has hydrogens To change this set reduce molecule updates current t and that as you can guess replaces rather than adds to the probed molecule This gives a static view of the molecule s interactions To get a dynamic view which is currently only enabled on rotating chi angles add these to your coot file set do probe dots on rotamers and chis 1 To get a semi static view dots are regenerated in the region of zone after a Real Space Refinement set do probe dots post refine 1 7 8 GLN and ASN B factor Outliers It is often difficult to detect by eye the correct orientation of the amino carbonylo group of GLN and ASNs However we can use properly refined temperature factors to detect outliers We take the Z value as half the difference between the B factor of the NE2 and OE1 divided by the standard deviation of the B factors of the rest of the residue An analysis of GLNs and ASNs of high resolutions structures indicates that a Z value of greater than 2 25 indicates a potential if not probable flip A Fix button is provided in the resultant dialog make this easy to do 5 and remember to check the difference map button in the Run Refmac dialog Chapter 7 Validation 58 This analysis was added after discussions with Atsushi Nakagawa and so is called Nak agawa s Bees The analysis does not check residues with multiple conformations 7 9 Validation Graphs Coot p
80. them can be found at the end of this manual 6 British modelling of course Chapter 3 General Features 12 Commands described throughout this manual such as vt surface 1 can be eval uated directly by Coot by using the Scripting Window Calculate gt Scripting Note that you type the commands in the upper entry widget and the command gets echoed in red and the return value and any output is displayed in the text widget lower green The typed command should be terminated with a carriage return Files can be evaluated executed using Calculate Run Script Note that in scheme the usual scripting language of Coot the parentheses are impor tant To execute a script file from the command line use the script filename arguments except when also using the command line argument no graphics in which case you should use s filename After you have used the scripting window you may have noticed that you can no longer kill Coot by using Ctrl C in the console To recover this ability exit in the scripting window 3 10 1 Python Coot has an optional embedded python interpreter Thus the full power of python is available to you Coot will look for an initialization script HOME coot py and will execute it if found This file should contain python commands that set your personal preferences 3 10 1 1 Python Commands The scripting functions described in this manual are formatted suitable for use
81. to generic object add dashed line 168 to generic object add display list handle WEE 170 to generic object add line 168 to generic object add point 169 toggle active mol niria reni a aonn eee eee 205 toggle display map eee 205 toggle display mol suus 205 toggle idle rock function 73 toggle idle spin function 73 transform coords molecule 206 transform map ic Sue iA Rees es a ris 206 transform map using lsq matrix 206 Lransform molecule by 112 Lranslate mnolecule by 112 translation bos a td de 205 Lrim m0olecule bu map 154 try set draw baton o0 IR eesti es 151 turn off backups isse der a poete aid 82 turn on backups nre dese sit di 82 U undo last moYe ioesee e tle AEN ears 112 undo symmetry view 0 6 cece eee eee 97 unique date time str 0000 204 unmangle hydrogen name s 172 unpathed backup file names state 83 unset dots colour iios rk eee eee 142 unset sticky sort by date 66 unskeletonize map cece cece 110 update go to atom from current atom 209 update go to atom from current position 227 update go to atom window on changed mol A rd M eU EIS eT ED cedo 114 update go to atom window on new mol 114 pdate self l2 son LB WE EUR 211 use graphics interface state
82. view set h bond dist max fle view set h bond dist max h bond dist max function Where h_bond_ dist_max is a number set the maximum considered hydrogen bond distance default 3 9 A 11 107 LSQ improve 11 107 1 lsq improve lsq improve imol ref ref selection imol_moving moving selection n res function dist_crit Where e mol_ref is an integer number e ref selection is a string e imol moving is an integer number Chapter 11 Scripting Functions e moving_selection is a string e n res is an integer number e dist_crit is a number 177 an slightly modified implementation of the lsq_improve algorithm of Kleywegt and Jones 1997 Note that if a residue selection is specified in the residue selection s then the first residue of the given range must exist in the molecule if not then mmdb will not select any atoms from that molecule Kleywegt and Jones set n_res to 4 and dist_crit to 6 0 11 108 single model view 11 108 1 single model view model number single model view model number mol imodel Where e mol is an integer number e model is an integer number put molecule number imol to display only model number imodel 11 108 2 single model view this model number single model view this model number mol Where mol is an integer number the current model number being displayed return 0 on non multimodel molecule 11 108 3 single model view next model number single model view next model numbe
83. 00 cece eee 194 refine active residue 00 196 refine active residue generic 196 refine active residue triple 196 refine auto range liess 121 refine with torsion restraints state 120 Hef ine Zone file RI dog rere 121 refine zone atom index define 121 refine zone with full residue spec scm 182 refinement immediate replacement state 119 refinement move atoms with zero occupancy State rras eoo aed haan hess cot 81 refinement refine per frame state 122 refmac calc sfs make mtz ss 185 refmadc zexe 6 Sigal Niche iv Debe LIE 196 refmac extra params sse sss 196 refmac name vero aes oil ea eae ee 95 refmac pDroblens geui sess 192 regularize zone eese 121 rem arks dialog ci pylllg tok yin ERR ons 69 remove coordinates glob extension 65 remove data glob extension 65 remove dictionary glob extension 66 remove map glob extension 66 remove named view eee 132 remove omega torsion restriants 119 remove planar peptide restraints 119 remove text 2 ones edie gas eae ees 175 remove vlew jee ita i renei Hi Sane SR See ee 132 rename residue gui 0 eee eee eee 191 Tender Marea 197 renumber residue TaOge oooocoooooococccooo 117 reorder chains 0 lc b cda xd 206 replace fragment sss sess 75 res spec chain id cece ee
84. 0000 e cece eens 146 11 67 5 delete atom 2 0 cece een rr 146 11 67 6 delete residue sidechain 0 000 cece eee eens 146 11 67 7 delete hydrogens 0 0 cece cece eee eee ees 147 11 68 Mainchain Building Functions 00 e eee 147 I1 68 db ri aimchain ve oii one Sacer Rete Re cde 147 xvii 11 69 Rotatmer Functions 0 eee eee 147 11 69 1 set rotamer search mode 0 0 cece eee eee eee 147 11 69 2 set zotamer Joweszt probabiltta 147 11 69 3 set rotamer check clashes 0 000 cee eee 147 11 69 4 auto fit best rotamer cece eee eee eee eee 148 11 69 5 set auto fit best rotamer clash flag ooooooooo o 148 11 69 06 MANETS 2 12 84b hoa weeds ent Ad eer eee teens 148 11 69 7 set residue to rotamer number 0000e eee 148 11 69 8 fill partial residues lesse 149 11 70 180 Flip Side chan 149 11 70 1 do 180 degree side chain flip 0 00 eee eee eee 149 11 71 Mutate bunctions 0 cece cee eee eens 149 11 71 1 setup mutate auto fit 2 00 eee eee eee 149 11 71 2 mutate ia dean eens 149 LLTI 3 mu tate ba se ir e eee al Bes ch 150 11 71 4 set mutate auto fit do post refine 00 2 ee 150 11 71 5 mutate auto Dt do Dost rebne state 150 11 71 6 set rotamer auto fit do post refine s sssesususs 150 11 71 7 rotamer auto Dt do Dost rebne state 150 11 71 8 mutate single residue by serial number 150 11 71 9 set residue type
85. 1 degrees You can change this using set colour map rotation for map step 3 actually it s a box in a coot difference map you will get to see the negative level contoured at the inverted level of the positive level what I mean is that you don t want to see the positive level going less than 0 5 takes you right back to the good old Frodo days no Chapter 6 Map Related Features ol 6 8 Difference Map Colouring For some strange reason some crystallographers like to have their difference maps coloured with red as positive and green as negative this option is for them set swap difference map colours 1 This option will allow the blue is positive red is negative colour scheme on Edit gt Map Colour 6 9 Make a Difference Map Using the Make a Difference Map function in the Extensions menu one can make a difference from two arbitrary maps The maps need not be on the same griding or in the same space group even The resulting map will be on the same griding and space group as the Reference map 6 10 Make an Averaged Map There is a scripting interface to the generation of map averages As above the maps need not be on the same grid or in the same space group The resulting map will have the same gridding and space group as the first map in the list Typical usage average map 1 1 0 2 1 0 The argument to average map is a list of lists each list element is a list of the
86. 1 m22 m23 m31 m32 m33 t1 t2 t3 Where e imolis an integer number this chain id is a string target chain id is a string mii is a number m12 is a number m13 is a number m21 is a number m22 is a number m23 is a number m31 is a number m32 is a number 158 function function Chapter 11 Scripting Functions 159 e m33 is a number e tl isa number e 2 is a number e t3 is a number add an NCS matrix for strict NCS molecule representation for CNS strict NCS usage expand like normal symmetry does 11 81 8 show strict ncs state show strict ncs state imol function Where mol is an integer number return the state of NCS ghost molecules for molecule number imol 11 81 9 set show strict ncs set show strict ncs imol state function Where e mol is an integer number e state is an integer number set display state of NCS ghost molecules for molecule number imol 11 81 10 set ncs homology level set ncs homology level flev function Where flev is a number At what level of homology should we say that we can t see homology for NCS calcu lation default 0 8 11 81 11 copy chain copy chain imol from_chain to_chain function Where e mol is an integer number e from chain is a string e to_chain is a string Copy single NCS chain 11 81 12 copy from ncs master to others copy from ncs master to others imol chain_id function Where e imolis an integer number e chain id is a string
87. 105 set density size csse 91 set diff map iso level increment 8T set display control dialog position 105 set display generic object 170 set display intro string 92 set display lists for maps 167 Set do anti aliasing oc e iriiretke tena 72 set do GL lighting eogi ei eee eee 72 set do probe dots on rotamers and chis 172 set do probe dots post refine 172 Set dots ColOr s ud se EPI ust s uei 198 set dots c lour iol a kn Ete ais 142 set dragged refinement steps per frame 122 set draw crosshairs se 152 set draw hydrogens sss 139 Function Index set draw map standard lines 76 set draw ncs ghosts sess 157 set draw solid density surface 76 set draw zero occ markers 139 set edit chi angles dialog position 106 set environment distances distance limits EE 126 Set egoteric deptbh cue 92 set fffear angular resolution 167 set filter fileselection filenames 66 set find hydrogen torsion 185 set find hydrogen torsions 153 set find ligand mask waters 135 set find ligand n top ligands 134 set fix chiral volumes before refinement EE 122 set flat shading for solid density surface A bua e PRAE 77 s t font color ossi pre a te 198 Set font COlOuE EE 107 S t fOnt size ue be weh s I
88. 108 11 31 4 set reset b factor moved atoms sees 108 11 31 5 get reset b factor moved atoms state sess 108 11 31 6 set atom attribute 0 cee cee ee 108 11 31 7 set atom string attribute 0 eee eee 109 11 31 8 set residue name 6 cece ese 109 11 32 Skeletonization Interface 109 11 32 1 zkeletonize map 2 00 e cece eee eee eens 109 11 32 2 unskeletonize map 0 000 e cece e ees 110 11 32 3 set max skeleton search depth eee ee 110 11 32 4 set skeleton box size sse 110 11 33 Read Mapsu i uere ERR Ria 110 11 33 1 handle read ccpiman eee eee eee 110 11 34 Save Coordmate 0 cece eee 110 11 34 1 save coordinates sss nne 110 11 35 Read Phases File Functions 00 e eee cece ee 111 11 35 1 read phs and coords and make map Les 111 11 35 2 read phs and make map using cell symm from previous mol eoe hte tuse user tU EP M ROS EIE 111 11 35 3 read phs and make map using cell symm from mol 111 11 35 4 read phs and make map using cell symm 111 11 35 5 read phs and make map with reso limits 112 11 36 Graphics Move sssssessssseses e 112 11 36 1 undo last move ssssssessese e en 112 11 36 2 translate molecule by 00 0 0c cee eee eee eee 112 11 86 38 transform molecule by 0 00 eee eee eee eee 112 11 37 Go To Atom Widget Functions 0 02 00 eee 113 11 37 1 post
89. 11 Scripting Functions 136 e imol_ligand is an integer number e chain id ligand is a string e resno ligand is an integer number e ins code ligand is a string e imol reference is an integer number e chain id reference is a string e resno reference is an integer number e ins_code_reference is a string Overlap residue with template based matching Overlap the first residue in mol ligand onto the residue specified by the reference parameters Use graph matching not atom names Match ligand atom names By using graph matching make the names of the atoms of the given ligand residue match those of the reference residue ligand as closely as possible where there would be a atom name clash invent a new atom name Returns success status False failed to find residue in either imol ligand or imo ref If success return the RT operator 11 60 13 flip ligand flip ligand imol chain id resno function Where e imol is an integer number e chain id is a string e resno is an integer number flip the ligand usually active residue around its eigen vectors to the next flip number Immediate replacement like flip peptide 11 61 Water Fitting Functions 11 61 1 execute find waters real execute find waters real imol for map imol for protein function new waters mol flag sigma_cut_off Where e imol for map is an integer number e imol for protein is an integer number e new waters mol flag is an integer number
90. 11 13 10 unpathed backup file names state oooooocooooocooo 83 11 13 11 backup compress Dles ztate s n un usune 83 11 13 12 set backup compres Dies 83 11 14 Recover Session Function 000 e cece eens 83 11 14 1 recover session 0 cece cee nnn 83 FEH Map FUCSIA adhd one eed S 83 11 15 1 calc pnhasen generic eee eee 83 11 15 2 map from mtz by refmac calc phases ssse 84 11 15 3 map Prom mtz bn cale phageg 0 0 cece eee eee 84 11 15 4 zet scrollwbheetmap cece e eee 84 11 15 5 zet scrollable map eee 84 11 15 6 serollwheelmgap eee eens 84 11 15 7 save previous map colour 0c cece eee esee 85 11 15 8 restore previous map colour ooooooccccconccccn ccoo 85 11 15 9 set active map drag flag 2 0 85 11 15 10 get active map drag flag 00 e eee eee 85 11 15 11 set last map colour 2 6 cece cece eee eee ee 85 11 15 12 set map colour 0 0 cece eee 85 11 15 13 set last map sigma step 00 c cece eee eee eee 85 11 15 14 zet contour be aiema Step be m0ol 86 11 15 15 data resohution 0 000 eee 86 11 15 16 modetresohutton 0 00 cece cee cee eens 86 HIH export m p i i i ra deena 86 11 15 18 export map fragment esses 86 11 15 19 differenc mapi ia ERE I IRE ug 87 11 16 Density Incerement rr 87 11 16 1 set iso level increment 0 cece eects 87 11 16 2 set diff map iso level increment sssssususur urnen 87
91. 11 79 Ll Tati di ii ess c e bre beret Ra 154 11 79 2 set raster3d bond thickness 0000 e eee eee 155 11 79 38 set raster3d atom radius 0 c cece eee 155 11 79 4 set raster3d density thickness 00 eee eee 155 11 79 5 set renderer show atoms sese 155 11 79 6 zet raster d bone rbickuesg 00 0 e ee eee eee 155 11 79 7 set raster3d shadows enabled cece eee ee 155 11 79 8 set raster3d water sphere 0 0 e eee eee eee eee 155 11 79 9 raster acreen zbot 0 00 eee ee 155 11 80 Superposition S5 ND o esas dE dut e tale in 156 IESO L puper POSE e228 etic taa 156 11 80 2 superpose with chain selection 0ooooooccooomm 156 11 80 3 ouperpose aith atom selection 0c eee eee 156 1U81 NOS td sede aes 157 11 81 1 set draw ncs ghosts ees 157 11 81 2 draw ncs ghosts state 0 0 cee eee eens 157 11 81 38 set ncs ghost bond thickness 00 02 eee e ee 157 11 81 4 nes update ghoets 0 0 cece cence eee 157 11 81 5 make dynamically transformed ncs maps 157 11 81 6 add nes matrix 0 0 cece eee eee 158 11 81 7 add strict nces matrix 00 158 11 81 8 show strict ncs state 0 cece eee eee 159 11 81 9 set show strict ncs 6 6 cece cee eee eens 159 11 81 10 set ncs homology level 0c c cece eee eee es 159 LESLIT scopy chain parao ease Teod 159 11 81 12 copy from ncs master to others eee eee 159 11 81 13 copy residue range f
92. 13 222 mutate auto fit do post refine state 150 mutate base Ie eas VI Lat a eI 150 mutate by overlap eee 209 mutate chain hes iu eun o ie xu west 213 mutate residue range less 213 mutate residue redundant 213 mutate single residue by serial number 150 mg button callback esses 197 ny top levelt v tin 197 N Eben 98219 Pee OP Oe A eee 68 Ee EE 143 AA hehe BEE ghee eae E 68 ke TE EE 69 n EE 148 N SYMOPS aid a id epit 99 ncs control change ncs master to chain 160 ncs control change ncs master to chain id e eux e ML UT card 160 ncs control display chain 160 ncs ligand oi a eas 191 ncs master chain id 00008 191 ncs update ghosts sess 157 new generic object number 168 new molecule by atom selection 163 new molecule by residue type selection 163 new molecule by smiles string 210 new molecule by sphere selection 163 new molecule by symmetry esses 98 new molecule by symmetry with atom Selection ca a au er GV 98 new molecule by symop sss 99 n0 cOOtcbtlpSutesscee e erm ra 198 notifv of nev vereion 197 nudge screen centre gui o oooooocoooooo 190 number rist aa A taka aad os 202 number of generic objects 170 O Ada in ad 128 open coords dialog 0 cece eee eee 66 open coot listener socket
93. 55 7 2 Geometry Analysis 0 00 e cece eee nes 55 7 3 Chiral Volumes EE E hh 55 7 3 1 Fixing Chiral Volume kor 56 7 4 Blobs a k a Unmodelled dente 56 7 5 Difference Map Peak 56 7 6 Check Waters by Difference Map 56 7 7 Molprobity Tools Interface 57 7 8 GLN and ASN B factor Outliers 0 00 cece ccc eee ee 57 7 9 Validation Graphs 0 00 e cece e 58 7 9 1 Residue Density nt 58 7 9 2 Rotamer Analysis e 58 7 9 3 Temperature Factor Vanance suussussraes eneon 58 7 9 4 Peptide Omega Angle Distortion o oo ooommmo o o 58 8 Representation 0 59 eS c c Ne eL he tl dede tate ut RUE Ok 59 9 Hints and Usage Tips 60 Hl Documentation cere eet Ree eymesces aa ee ees 60 9 2 Low Resolution 252 evene eneet le bubs nee Id ERES 60 9 3 Coot Droppings esit narea A ta dada re des 60 9 4 Clearing Backup 61 9 5 Getting out of Translate Mode 61 9 6 Getting out of Continuous Rotation Mode 61 9 7 Getting out of Label Atom Only Mode 61 9 8 Button Labels Zeeche ebe PUDE UE DUE ENS 61 0 0 T PACKING aceto trema botte tale cents tette inlets 61 9 10 Resizing Vi War rx ERR Cere RENE RE E 62 91 1 SerolEwheel ii ete os Steen eet 62 9 12 Slow Computer Configuration ssssseseses rreren 62 10 Other EE Vilca wontons PEUX 63 US Wee 63 11 Scripting Functions 64 11 1 The Virtual Trackball cc 64 LIII Visado dara sae oo
94. 6S rci tem Orne Ctr e RR eee 191 13 13 SheBt cci ert REI ua wORekLREe E elu RU beris 192 13 14 ehat check sl rr rtr 192 13 15 refmac problemsg eh 192 19 10 pete Dikara ede pe A ete enhn pd 192 13 17 br teslsqmats i obest et Febre t T PR Eb ERES 193 13 18 eptre tdo button 0 cece nee eee eee ees 193 13 19 prodrg import edesin ea A E e ees 193 13 20 foscnatmg hungs 0 ccc cece eee eens 193 US DEG Me 193 13 22 generiec obhiects re 194 13 29 TIUUIT Bue testate tee NEU ter hen REM 195 13 24 TOMA RA RI EGLI DEL MESI E DE 196 13 29 8crApper gul c hae ee Pa baa dee ER 197 13 26 evtra Lop Jevel eee 197 13 27 raster3d from scheme 0c ec eese eese 197 13 28 checkJor updates rr 197 13 29 mutate from scheme 0000s cece ect een 198 13 30 PS Aen HR err e cette Ub sea Veces nie 198 13 31 AMETICADISMS bled a ae dt ee een da 198 13 32 exercise scM MOl ceray i ccc ens 198 13 33 r motescorntrol Di tee ahve eee tee ees 199 WS OAs EE Sie um ea Soke e A Mh ts tak ede de lt Ao en 199 13 35 Della ead Sid dane RC hh on She 200 13 36 parse pisa xml 0 ccc eee en 200 I9 37 COOTHIUIS crates ner eredi tet ka dot bea tt en in sciat 201 13 38 enartcookt docg ee sad ann 211 13 39 pS B luu e Chee DW Re Nu eset reet 212 13 40 backeround demo 2 0 0 cece cece ee ne 212 13 41 coot crash catcher oeron eaaa ccc cee eee ene 212 13 42 mutate An Scheme 060 EEEE E EVANSA 213 13 43 CO let a Ga Seed aad
95. 72 USCLTMOAS PU eii id pes 191 V KEE 90 valid mnap mnolecule suus 207 valid mnodel a0oleculen ooo 206 valid refinenent map sess 207 viewcmatrix id nes 205 view quaternion see 205 view saver gui lle 190 views panel gui 6 eee eee eee 190 VE SUPLACE e Eege it ens 64 Wt surface status paris Mousa ge EV 64 W water chain from shelx ins scm 183 water chain SCm i b oss eR E ed ie 183 water coordination gui s s 191 vatson crilck pnair 0000 164 watson crick pair for residue range 164 write ccp4mg picture description 174 Ce le DEE 94 wrilte reduce het dict 194 write residue range to pdb file 94 grite sbhelz Ane file 129 Z zalman stereo mode eese 104 zoomn factorz x olenertexpesR yuaceqentusis 127
96. 87 2 set transparent electrostatic surface set transparent electrostatic surface imol opacity function Where e imolis an integer number e opacity is a number simple on off screendoor transparency at the moment an opacity gt 0 0 will turn on screendoor transparency stippling 11 87 3 get electrostatic surface opacity get electrostatic surface opacity imol function Where mol is an integer number return 1 0 for non transparent and 0 5 if screendoor transparency has been turned on 11 88 FFFearing 11 88 1 fffear search fffear search imol model imol map function Where e imol model is an integer number e imol map is an integer number fffear search model in molecule number mol model in map number imol map Chapter 11 Scripting Functions 11 88 2 set fffear angular resolution set fffear angular resolution f Where f is number set and return the fffear angular resolution in degrees 11 88 3 fffear angular resolution fffear angular resolution return the fffear angular resolution in degrees 11 89 Remote Control 11 89 1 make socket listener maybe make socket listener maybe try to make socket listener 11 90 Display Lists for Maps 11 90 1 set display lists for maps set display lists for maps i Where 1 is an integer number 167 function function function function Should display lists be used for maps It may speed things up if these are turned on or off depends on g
97. EBI server File gt Get PDB Using Code A pop up entry box is displayed into which you can type a PDB accession code Coot will then connect to the web server and transfer the file Coot blocks as it does this which is not ideal but on a semi decent internet connection it s not too bad The downloaded coordinates are saved into a directory called coot download It is also possible to download mmCIF data and generate a map This currently requires a properly formatted database structure factors mmCIF file 4 7 Get Coordinates and Map from EDS Using this function we have the ability to download coordinates and view the map from structures in the Electron Density Server EDS at Uppsala University This is a much more robust and faster way to see maps from deposited structures This function can be found under the File menu item This feature was added with the assistance of Gerard Kleywegt If you use the EDS please cite GJ Kleywegt MR Harris JY Zou TC Taylor A Wahlby amp TA Jones 2004 The Uppsala Electron Density Server Acta Cryst D60 2240 2249 that also only makes sense in the region of the reference chain 5 OCA is goose in Spanish and Italian D the default is the Weizmann Institute which for reasons I won t go into here is currently much faster than the EBI server 7 which currently only a fraction are Chapter 4 Coordinate Related Features 22 4 8 Save Coordinates On selecting fro
98. MS 107 set go to atom chain residue atom name 113 set go to atom molecule 114 set go to atom window position 105 set graphics window position 104 set graphics window size 104 set hardware stereo angle factor 105 set have unsaved changes 82 set idle function rotate angle 73 set imol refinement map 123 set interactive probe dots molprobity TAGIUS wits ere ger RM Ier 172 set iso level increment 87 set keep map colour after refmac 95 set kleywegt plot n diffs 129 set last map color sese 198 set Ila st map COlOUE eieefestenkerlir uie 85 set last map contour level 88 set last map contour level by sigma 88 set last map sigma step sess 85 set ligand acceptable fit fraction 134 set ligand cluster sigma level 134 set ligand flexible ligand n samples 134 set ligand search map molecule 135 set ligand search protein molecule 135 set ligand water n cycles 137 set ligand water to protein distance limits A ei ete eRe ate 137 set map colour i seg 4 be oda 85 set map displayed sse 115 set map is difference map 92 set map line width sess 89 set map mask atom radius 153 set map radiusi s ed da eee
99. Note mol cen could contain values less than 9999 move molecule to screen centre imol Move the centre of molecule number imol to the current screen centre move molecule here This is a short name for the above move molecule to screen center this is an americanism identity matrix Return a nine membered list of numbers translation axis length e g translation x 2 gt 2 0 0 Return scheme false on error rotate about screen axis axis degrees Rotate degrees about screen axis where axis is either x y or z toggle display map imol idummy 205 procedure procedure procedure procedure procedure procedure procedure procedure procedure procedure procedure procedure procedure procedure Support for old toggle functions consider instead the raw functions use the direct set_displayed functions toggle display mol imol toggle the display of imol toggle active mol imol toggle the active state clickability of imol procedure procedure Chapter 13 Scheme Scripting Functions 206 scheme representation imol procedure return a scheme representation of molecule imol or f if we can t do it imol is a map say reorder chains imol procedure reorder chains transform coords molecule imol rtop procedure transform a coordinates molecule by a coot rtop which is a SCM expression of a clipper RTop i e a list of a 9 element list and a 3 element lis
100. Positions in 3D space can be annotated with 3D text The mechanism to do this can be found under Extensions gt Representations gt 3D Annotations 3D Annotations can be saved to and loaded from a file 3 24 Frame Rate Sometimes you might as yourself how fast is the computer Using Calculate gt Frames Sec you can see how fast the molecule is rotating giving an indication of graphics performance It is often better to use a map that is more realistic and stop the picture whizzing round The output is written to the status bar and the console you need to give it a few seconds to settle down It is best not to have other widgets overlaying the GL canvas as you do this The contouring elapsed time gives an indication of CPU performance 3 25 Program Output Due to its in development nature at the moment Coot produces a lot of console output much of it debugging or informational This will go away in due course You are advised to run Coot so that you can see the console and the graphics window at the same time since feedback from atom clicking for example is often written there rather than displayed in the graphics window e Output that starts ERROR is a programming problem and ideally you should never see it e Output that starts WARNING means that something probably unintended hap pened due to the unexpected nature of your input or file s e Output that starts DEBUG has o
101. The Coot User Manual Paul Emsley paul dot emsley at bioch dot ox dot ac dot uk b Table of Contents 1 o Te EE 1 1 1 Citing Coot and Hiends eee eee 1 1 2 What is Coot waco eye eens pee inen e Soa dsb eld teense 1 1 3 What Coots NOb i i ito eser gp oie ret pala Aah ake sakes 1 1 4 Hardware Reouirementa 0000 rererere e nee ee 2 LATE Mo AD BEE AS 2 1 5 Environment Variables oocooccccccoccccoooccccnoncccc 2 1 6 Command Line Arguments eee 3 Lit Web Pagecnoueeec t A epp ELE 4 Te Cras ite nope A fs Lut dre 4 Mousing and Keyboarding 5 2 T Next Residue ea da a aha ate 5 2 2 Keyboard Contouring e erer ereen cece een eee eens 5 2 3 Mouse Z Translation and OChponmg cee eee eee 5 2 4 Keyboard Translation 6 2 5 Keyboard Zoom and Op 6 2 6 crol wheel eR RI RE I es 6 2 7 Selecting Atomis rerin A RR ERU e ne RR ERR EE Ed 6 28 Virtual Trackball duri ES A Nah ea ee E PE EU ege 6 2 9 More or Zooming c c eb A AR e s T General Features 8 3 L Version number ssepe sb e er RU eei 8 332 Antialiasing cene iueeeso a Dp ban 8 3 3 Molecule Number 8 3 4 Display Issues d sioe lali 9 SAA IUE 9 9452 Pick rSoDuegne EXER Hx 9 3 4 3 Origin Marker 0 c cece enn 9 3 5 jScreensliob eevee donee atu nda eae ear UON eM hee 9 3 6 Raster3D Outputs meca paros 10 3 7 Display Manager 10 3 8 The Modelling Toolbar 0 0 00 cece eee eee 11 3 9 The file selector ssec et car
102. This interface will not change residues with insertion codes or alternate conformation The lowest rotamer probability is set to 0 01 5 13 Editing chi Angles Instead of using Rotamers one can instead change the x angles often called torsions by hand using Edit Chi Angles from the Model Fit Refine dialog To edit a residue s x1 press 1 to edit xa 2 X3 3 and x4 4 Use left mouse click and drag to change the x value Use keyboard 0 to go back to ordinary view mode at any time during the editing Alternatively one can use the View Rotation Mode or use the CTRL key when moving the mouse in the graphics window Use the Accept Reject dialog when you have finished editing the x angles 21 The Backrub Motion How Protein Backbone Shrugs When a Sidechain Dances Structure Volume 14 Issue 2 Pages 265 274 I Davis W Bryan Arendall III D Richardson J Richardson 22 for example in preparation of a model for molecular replacement 23 atoms of residues that are too close to each other 24 that s zero Chapter 5 Modelling and Building For non standard residues the clicked atom defines the base of the atom tree which defines the head of the molecule it s the tail twigs leaves that wags To emphasise then it matters on which atom you click By default torsions for hydrogen atoms are turned off To turn them on set find hydrogen torsions 1 To edit the rotatable bond
103. Where e mtz_file name is a string e ais a string e bis a string e weight is a string e use_weights is an integer number e is diff map is an integer number e have refmac params is an integer number Chapter 11 Scripting Functions fobs_col is a string sigfobs_col is a string r_free_col is a string sensible_f_free_col is an integer number as the above function execpt set refmac parameters too pass along the refmac column labels for storage not used in the creation of the map Returns 1 on error else return imol 11 17 5 make and draw map with reso with refmac params make and draw map with reso with refmac params mtz_file_name function a b weight use weights is diff map have_refmac _ params fobs col sigfobs_col r free col sensible f free col is anomalous use reso limits low reso limit high reso lim Where mtz_file_name is a string a is a string b is a string weight is a string use_weights is an integer number is diff map is an integer number have refmac params is an integer number fobs_col is a string sigfobs_col is a string r_free_col is a string sensible_f_free_col is an integer number s_anomalous is an integer number use_reso_limits is an integer number low reso limit is a number high_reso_lim is a number as the above function except set expert options too 11 17 6 valid labels valid labels mtz file name f_col phi_col weight_col use weights Where mtz
104. _file_name is a string f col is a string phi_col is a string weight_col is a string use_weights is an integer number does the mtz file have the columms that we want it to have function Chapter 11 Scripting Functions 91 11 17 7 auto read make and draw maps auto read make and draw maps filename function Where filename is a string read MTZ file filename and from it try to make maps Useful for reading the output of refmac The default labels FWT PHWT and DELFWT PHDELFWT can be changed using something Returns the molecule number for the new map 11 17 8 set auto read do difference map too set auto read do difference map too i function Where i is an integer number set the flag to do a difference map too on auto read MTZ 11 17 9 auto read do difference map too state auto read do difference map too state function return the flag to do a difference map too on auto read MTZ Returns 0 means no 1 means yes 11 17 10 set auto read column labels set auto read column labels fwt phwt is for diff map flag function Where e but is a string e phwt is a string e is for diff map flag is an integer number set the expected MTZ columns for Auto reading MTZ file Not every program uses the default refmac labels FWT PHWT for its MTZ file Here we can tell coot to expect other labels so that coot can Auto open such MTZ files e g set auto read column labels 2FOFCWT PH2FOFCWT 0 11 17 11 se
105. _y1 is a number e normal_z1 is a number add point to generic object object number Chapter 11 Scripting Functions 11 92 6 to generic object add display list handle to generic object add display list handle object_number display_list_id Where e object number is an integer number e display list id is an integer number add a display list handle generic object 11 92 7 set display generic object set display generic object object number istate Where e object number is an integer number e state is an integer number set the display status of object number object number 170 function function when they are created by default objects are not displayed so we generally need this function 11 92 8 generic object is displayed p generic object is displayed p object number Where object number is an integer number is generic display object displayed Returns 1 for yes otherwise O 11 92 9 generic object index generic object index name Where name is a string return the index of the object with name name if not return 1 11 92 10 number of generic objects number of generic objects what is the name of generic object number obj number return the number of generic display objects Returns 0 NULL scheme False on obj_number not available 11 92 11 generic object info generic object info function function function function print to the console the name and display stat
106. a 79 11 9 20 suck model fit dialog 0 0 cece eee eens 80 11 9 21 add status bar text 0 0 cece cece eee eee eee 80 11 10 Mouse Buttons cc eis as 80 11 10 1 set control key for rotate cesses 80 11 10 2 control key for rotate state csse 80 11 10 3 blob under pointer to screen centre sssssssse 80 11 11 Cursor Function zr e e aen 80 11 11 1 set pick cursor index 0 00 cece eens 80 11 12 Model Fit Refine Functions 5 e beet tei ciate Aa get 81 11 12 1 post model fit refine dialog 0 cece eee ee eee 81 11 12 2 show select map dialog sese 81 11 12 3 set model fit refine rotate translate zone label 81 11 12 4 set model fit refine place atom at pointer label 81 11 12 5 post other modelling tools dialog 0ooooomoom o 81 11 12 6 set refinement move atoms with zero occupancy 81 11 12 7 refinement move atoms with zero occupancy state 8l 11 13 Backup Functions ee e 81 11 13 1 makebackun 0 cc cece cece a a e eee 81 11 13 2 rurm oft backun eee nee eee 82 11 13 38 Turm on backup eens 82 11 13 4 backup state cece eee eee eee eens 82 11 13 5 set have unsaved changes eee eee eee eens 82 11 13 6 have unsaved changes p 0 e cece e eee eee ees 82 11 13 7 set undo molecule 0 82 11 13 8 show set undo molecule chooser 0 20 eee eee 82 11 13 9 set unpathed backup file names 0 00000 83
107. a ia 5T reference manual 1 reference structure 2 refine single check 27 A tA bue EA EET dle 27 refinement weight 27 refinement rigid body 0 30 refinement simples sssssrererererrrrrrrnn 31 refining residues soe ie WM ls 29 refmac zoe woo URLs Se vue e d TEE ad 43 refmac map Colour 00 eee e eee eee eee 43 refmac parameters cee eee nee 43 refmac default 43 FegularizatlioMi 22 ee ENN Bed el AEN bes 27 Fender EEN rr TEIG ES 10 renumbering residues ooocococccoccccccccco 38 residue dno ica caidos 19 PESIZING EE 62 restore after crash ccc cece eee eee eee 14 reverse direction 33 tieid Dody ltda Mocks reise 30 RNA ideal uno tei di gei uer H 42 RNA TEE 37 Concept Index TOLIMA RS A era WERE YR 34 rotate translate manual 30 enee EE 15 rotation centre Dointer ee eee eee 16 r nning Tefmac pico japos 43 running SHEL XL 6 eis nites es estes ee shee 44 S save coordinates directory oooooooooommm 11 SCHEME AS 12 BOTES Oi As 9 SAP ti AA bale ee 11 A wand saw teg Rises RES E E dere 10 scroll wheel map bor 62 scroll map contour change by 6 scrol wheel rro 6 Secondary Structure Matching SSM 24 sequence view 23 Ge Eh setae stews elt EY REV O 27 set rotation centre 6 6 eee eee eee 15 setting space group sseeeee 02 22 sharpening map 52 SHELX MMS eR RA REP Vou fx 18 A noyer et pee aere ete 44
108. a string e chain imol2 is a string e chain used flag mol is an integer number e chain used flag imol2 is an integer number e move imol2 copy flag is an integer number chain based interface to superposition Superpose the given chains of imol2 onto moll moll is reference we can either move imol2 or copy it to generate a new molecule depending on the vaule of move imol2 flag 1 for move 0 for copy 11 80 3 superpose with atom selection superpose with atom selection imoll imol2 mmdb atom sel str 1 function mmdb atom sel str 2 move imol2 copy flag Where e imoll is an integer number e imol2 is an integer number e mmdb_atom_sel_str_1 is a string e mmdb_atom_sel_str_2 is a string e move_imol2_copy flag is an integer number Chapter 11 Scripting Functions 157 detailed interface to superposition Superpose the given atom selection specified by the mmdb atom selection strings of imol2 onto moll moll is reference we can either move mol or copy it to generate a new molecule depending on the vaule of move_imol2_flag 1 for move 0 for copy Returns the index of the superposed molecule which could either be a new molecule if move_imol2_flag was 1 or the imol2 or 1 signifying failure to do the SMM superposition 11 81 NCS 11 81 1 set draw ncs ghosts set draw ncs ghosts imol istate function Where e mol is an integer number e state is an integer number set drawing state of NCS ghost
109. ac there should be relatively unbiased density in the resulting 2Fo Fc style and difference maps Similarly there is a function to reverse this operation e fill occupancy residue range imol chain id resno start resno last 5 40 Fix Nomenclature Errors Currently this is available only in scripting form fix nomenclature errors imol This will fix atoms nomenclature problems in molecule number imol according to the same criteria as WATCHECK e g Chi 2 for Phe Tyr Asp and Glu should be between 90 and 90 degrees Note that Val and Leu nomenclature errors are also corrected 5 41 Rotamer Fix Whole Protein There is an experimental scripting function fit protein imol which does a auto fit rotamer and Real Space Refinement for each residue The graphics follow the refinement 5 42 Refine All Waters All the waters in a model can be refined that is moved to the local density peak using fit waters imol This is a non interactive function the waters are moved without user intervention 5 43 Moving Molecules Ligands Often you want to move a ligand or some such from wherever it was read in to the position of interest in your molecule i e the current view centre There is a GUI to do this Calculate Move Molecule Here There are scripting functions available for this sort of thing molecule centre imol will tell you the molecule centre of the imolth molecule translate molecule by imol x shift y shift z
110. ackball type 202 set water check spherical variance limit EE 137 set write conect record state 178 Setup mutate auto ZIt suss 149 Setup Lorglon general s 153 SAPO e EE EEN 172 shell command to file with data 203 shell command to string 203 shelx molecule esses 202 207 shelxl refine pie peii dri 192 shelxl refine primitive 192 Shorten Daton sn co eec uu rere cuu ut 152 show coot tip from list 212 show environment distances state 126 show main toolbar ees 79 show model toolbar all icons 79 226 show model toolbar main icons 79 Show modelling toolbar 79 Show origin marker state 79 Show partial charge info 173 show paths in display manager state 65 show pointer distances state 127 show select map dialoB oooooooooommmoo 81 Show set undo molecule chooser 82 Shoy epacCegtoub nnne 116 show strict ncs state sss 159 side by side stereo mode 104 simple lsq match sssseeeeeees 214 single manual ncs ghost 191 single model view model number 177 single model view next model number 177 single model view prev model number 177 single model view this model number 177 Skeletonize map eee
111. ad dade des 121 11 43 17 rebne auto range 6 eee e 121 11 43 18 regularize zone 2 0 cence teens 121 11 43 19 set dragged refinement steps per frame 122 11 43 20 dragged refinement steps per frame 45 122 11 43 21 set refinement refine per frame 000000 122 11 43 22 refinement refine per frame state oooooccccooom o 122 11 43 23 set rebne ramachandran angles 122 11 43 24 set fix chiral volumes before refinement 122 11 43 25 check chratvolumes anenee 122 11 43 26 set show chiral volume errors dialog oo o 123 11 43 27 set secondary structure restraints type 123 11 43 28 secondary structure restraints tyDO 0o oooooooo o 123 11 43 29 mmotrebnement map 0 ccc e eee eee eee 123 11 43 30 set imol refinement map 0 0 2 eee eee ee 123 11 43 31 does residue exist p 6 eee cece eens 123 11 43 32 add extra bond restraint esee 124 xiv 11 43 33 delete allectra restraints 124 11 43 34 delete extra restraints for Iesidue o ooooooooooo 124 11 44 Simplex Refinement Interface 125 11 44 1 fit residue range to map by simplex sss 125 11 44 2 score residue range fit to map 000 cee eee eee eee 125 11 45 Nomenclature Error 125 11 45 1 fix nomenclature errors sse 125 11 45 2 set nomenclature errors on read e 125 11 46 Atom Info Interface 126 11 46 1 output
112. ad of turning it off 3 15 Views Coot has a views interface you might call them scenes that define a particular ori entation zoom and view centre Coot and linearly interpolate between the views The animation play back speed can be set with the Views Play Speed menu item default is a speed of 10 The views interface can be found under the Extensions menu item 17 if no space group has been assigned it returns No spacegroup for this molecule Chapter 3 General Features 16 3 16 Clipping Manipulation The clipping planes a k a slab can be adjusted using Edit gt Clipping and adjusting the slider There is only one parameter to change and it affects both the front and the back clipping planes The clipping can also be changed using keyboard D and F It can also be changed with Ctrl Right mouse drag up and down Likewise the screen Z can be changed with Ctrl Right mouse left and right One can push and pull the view in the screen Z direction using keypad 3 and keypad gt see Section Section 2 4 Keyboard Z Translation page 6 3 17 Background colour The background colour can be set either using a GUI dialog Edit gt Background Colour or the function set background colour 0 00 0 00 0 00 where the arguments are 3 numbers between 0 0 and 1 0 which respectively represent the red green and blue compo nents of the background colour The default is 0 0 0 0 0
113. alculate SFs from an MTZ file and generate a map Returns the new molecule number 11 15 4 set scroll wheel map set scroll wheel map imap function Where imap is an integer number set the map that is moved by changing the scroll wheel and change contour level 11 15 5 set scrollable map set scrollable map imol function Where mol is an integer number return the molecule number to which the mouse scroll wheel is attached set the map that has its contour level changed by the scrolling the mouse wheel to molecule number imol same as Ji 11 15 6 scroll wheel map scroll wheel map function the contouring of which map is altered when the scroll wheel changes Chapter 11 Scripting Functions 11 15 7 save previous map colour save previous map colour imol function Where mol is an integer number save previous colour map for molecule number imol 11 15 8 restore previous map colour restore previous map colour imol function Where mol is an integer number restore previous colour map for molecule number imol 11 15 9 set active map drag flag set active map drag flag t function Where t is an integer number set the state of immediate map upate on map drag By default it is on t 1 On slower computers it might be better to set t 0 11 15 10 get active map drag flag get active map drag flag function return the state of the dragged map flag 11 15 11 set last map colour set last map colour fl f2 f3 fu
114. ally not use this but instead use is solvent chain imol chain id Returns 1 on error 0 for no 1 for is a solvent chain We wouldn t want to be doing rotamer searches and the like on such a chain 11 6 8 n residues n residues imol function Where mol is an integer number return the number of residues in the molecule return 1 if this is a map or closed 11 6 9 sort chains sort chains imol function Where mol is an integer number sort the chain ids of the imol th molecule in lexographical order 11 6 10 sort residues sort residues imol function Where mol is an integer number sort the residues of the imol th molecule 11 6 11 remarks dialog remarks dialog imol function Where mol is an integer number a gui dialog showing remarks header info for a model molecule 11 6 12 print header secondary structure info print header secondary structure info imol function Where mol is an integer number simply print secondardy structure info to the terminal console In future this could should return the info 11 6 13 copy molecule copy molecule imol function Where mol is an integer number copy molecule imol Returns the new molecule number Return 1 on failure to copy molecule out of range or molecule is closed Chapter 11 Scripting Functions 11 6 14 add ligand delete residue copy molecule add ligand delete residue copy molecule imol_ligand_new function chain id ligand new resno_
115. alse 12 7 6 residues near residue residues near residue imol residue_in radius function Where e imolis an integer number e residue in is a SCM e radius is a number return residues near residue Return residue specs for residues that have atoms that are closer than radius Angstroems to any atom in the residue specified by res in 12 8 Refinement with specs 12 8 1 refine zone with full residue spec scm refine zone with full residue spec scm imol chain id resnol function inscode_1 resno2 inscode_2 altconf Where e mol is an integer number e chain id is a string e resnol is an integer number e inscode_1 is a string e resno is an integer number e inscode 2 is a string e altconf is a string refine a zone allowing the specification of insertion codes for the residues too presumes that imol_Refinement_Map has been set 12 9 Water Chain Functions Chapter 12 More Scripting Functions 183 12 9 1 water chain from shelx ins scm water chain from shelx ins scm imol function Where mol is an integer number return the chain id of the water chain from a shelx molecule Raw interface Returns scheme false if no chain or bad imol 12 9 2 water chain scm water chain scm imol function Where mol is an integer number return the chain id of the water chain Raw interface 12 10 Spin Search Functions 12 10 1 spin search spin search mol map imol chain_id resno ins_code direction atoms list function
116. ame is a string is the given file name suitable to be read as coordinates 11 3 17 open coords dialog open coords dialog display the open coordinates dialog function function function function function function function function Chapter 11 Scripting Functions 11 4 Widget Utilities 11 4 1 info dialog info dialog txt function Where tzt is a string create a dialog with information create a dialog with information string txt User has to click to dismiss it but it is not modal nothing in coot is modal 11 4 2 info dialog and text info dialog and text txt function Where tzt is a string create a dialog with information and print to console as info dialog but print to console as well 11 5 MTZ and data handling utilities 11 5 1 manage column selector manage column selector filename function Where filename is a string given a filename try to read it as a data file We try as phs and cif files first 11 6 Molecule Info Functions 11 6 1 chain n residues chain n residues chain id imol function Where e chain d is a string e imol is an integer number the number of residues in chain chain id and molecule number mol Returns the number of residues 11 6 2 resname from serial number resname from serial number imol chain id serial num function Where e imol is an integer number e chain id is a string e serial num is an integer number return the rename fr
117. ap sampling rate function return the map sampling rate 11 16 5 change contour level change contour level is increment function Where is increment is an integer number change the contour level of the current map by a step if is_increment 1 the contour level is increased If is_increment 0 the map contour level is decreased Chapter 11 Scripting Functions 11 16 6 set last map contour level set last map contour level level function Where level is a number set the contour level of the map with the highest molecule number to level 11 16 7 set last map contour level by sigma set last map contour level by sigma n sigma function Where n_sigma is a number set the contour level of the map with the highest molecule number to n sigma sigma 11 16 8 set stop scroll diff map set stop scroll diff map i function Where 1 is an integer number create a lower limit to the Fo Fc style map contour level changing default 1 on 11 16 9 set stop scroll iso map set stop scroll iso map i function Where i is an integer number create a lower limit to the 2Fo Fc style map contour level changing default 1 on 11 16 10 set stop scroll iso map level set stop scroll iso map level f function Where f is number set the actual map level changing limit default 0 0 11 16 11 set stop scroll diff map level set stop scroll diff map level f function Where f is number set the actual difference map level changing lim
118. apter 11 Scripting Functions e resno is an integer number e ins code is a string e rotamer number is an integer number set the residue specified to the rotamer number specifed 11 69 8 fill partial residues fill partial residues imol Where mol is an integer number fill all the residues of molecule number imol that have missing atoms To be used to remove the effects of chainsaw 11 70 180 Flip Side chain 11 70 1 do 180 degree side chain flip do 180 degree side chain flip imol chain id resno inscode altconf Where e imolis an integer number e chain_id is a string e resno is an integer number e inscode is a string e altconf is a string rotate 180 degrees round the last chi angle 11 71 Mutate Functions 11 71 1 setup mutate auto fit setup mutate auto fit state Where state is an integer number Mutate then fit to map that we have a map define is checked first 11 71 2 mutate mutate imol chain_id ires inscode target_res_type Where e imol is an integer number e chain_id is a string e ires is an integer number e inscode is a string e target_res_type is a string 149 function function function function Chapter 11 Scripting Functions 150 mutate a given residue target_res_type is a three letter code Return 1 on a good mutate 11 71 3 mutate base mutate base imol chain_id res_no ins_code res_type function Where e mol is an integer number e chain id is a string e
119. apter 11 Scripting Functions 71 11 7 3 molecule name molecule name imol function Where mol is an integer number return the name of molecule number imol Returns 0 if not a valid name gt False in scheme e g a b c pdb for d e f mtz FWT PHWT 11 7 4 set molecule name set molecule name imol new name function Where e imol is an integer number e new name is a string set the molecule name of the imol th molecule 11 7 5 coot real exit coot real exit retval function Where retval is an integer number exit from coot give return value retval back to invoking process 11 7 6 first coords imol first coords imol function What is the molecule number of first coordinates molecule return 1 when there is none 11 7 7 first small coords imol first small coords imol function molecule number of first small 400 atoms molecule return 1 on no such molecule 11 7 8 first unsaved coords imol first unsaved coords imol function What is the molecule number of first unsaved coordinates molecule return 1 when there is none 11 7 9 mmcif sfs to mtz mmcif sfs to mtz cif file name mtz file name function Where e cif file name is a string e mtz_file name is a string convert the structure factors in cif file name to an mtz file Return 1 on success Return 0 on a file without Rfree return 1 on complete failure to write a file Chapter 11 Scripting Functions 11 8 Graphics Utility Function
120. ate it if needed Create another moecule called Reverse Helix if the helix orientation isn t completely unequivocal Returns the index of the new molecule 11 82 2 place strand here place strand here n residues n sample_strands function Where e n residues is an integer number e n sample strands is an integer number add a strands Add a strand close to this point in the map try to fit the orientation Add to a molecule called Strand create it if needed n_residues is the estimated number of residues in the strand n sample strands is the number of strands from the database tested to fit into this strand density 8 is a suggested number 20 for a more rigourous search but it will be slower Returns the index of the new molecule 11 82 3 place strand here dialog place strand here dialog function show the strand placement gui Choose the python version in there if needed Call scripting function display it in place don t return a widget 11 82 4 find helices find helices function autobuild helices Find secondary structure in the current map Add to a molecule called Helices create it if needed Returns the index of the new molecule 11 82 5 find strands find strands function autobuild strands Find secondary structure in the current map Add to a molecule called Strands create it if needed Returns the index of the new molecule Chapter 11 Scripting Functions 162 11 82 6 find secon
121. ate of the check button either t of f if check button label not a string then we don t display or create even the check button If it is a string create a check button and add the callback handle check button function which takes as an argument the active state of the the checkbutton molecule centres gui procedure A demo gui to move about to molecules old coot procedure old coot test interesting things gui title baddie list procedure We can either go to a place in which case the element is a list of button label string and 3 numbers that represent the x y z coordinates or an atom in which case the element is a list of a button label string followed by the molecule number chain id residue number ins code atom name altconf e g interesting things gui Bad things by Analysis X list list Bad Chiral 0 A 23 CA A list Bad Density Fit 0 B 65 CA list Interesting blob 45 6 46 7 87 5 interesting things with fix maybe title baddie list procedure In this case each baddie can have a function at the end which is called when the fix button is clicked fill option menu with mol options menu filter function procedure Fill an option menu with the right type of molecules If filter function returns t then add it Typical value of filter function is valid model molecule fill option menu with coordinates mol options menu procedure Helper function for molecule chooser Not really for
122. ates Thus you do not have to remember to Save Changes coot will do it for yout If you have made changes to more than one molecule Coot will pop up a dialog box in which you should set the Undo Molecule i e the molecule to which the Undo operations 9 10 11 in that particular directory funny that this might be initially surprising since this could chew up a lot of disk space However disk space is cheap compared to losing you molecule 12 13 The coordinates are written in pdb format that s OK isn t it unless you tell it not to of course use e g turn off backup 0 to turn off the backup for molecule 0 in this case Chapter 3 General Features 14 will apply Further Undo operations will continue to apply to this molecule until there are none left If another Undo is requested Coot checks to see if there are other molecules that can be undone if there is exactly one then that molecule becomes the Undo Molecule if there are more than one then another Undo selection dialog will be displayed You can set the undo molecule using the scripting function set undo molecule imol If for reasons of strange system requirements you want to remove the path components of the backup file name you can do so using set unpathed backup file names 1 3 11 1 Redo The undone modifications can be re done using this button This is not available imme diately after a modification 3 11 2
123. atom info as text csse 126 11 47 Residue Environment Functions suua sua ssnu esnan 126 11 47 1 set show environment distances 00000 eee 126 11 47 2 set show environment distances bumps 126 11 47 3 set show environment distances h bonds 126 11 47 4 show environment distances state oooooooocoooooo 126 11 47 5 set environment distances distance limits 126 11 48 Pointer bunctons 0 0 ccc ccc ccc hn 127 11 48 1 oet sbhow Doimnter dstancen 0 eee eee eee eee 127 11 48 2 show pointer distances state 00 c eee eee eee eee 127 11 49 Zoom Functions mossi 0 0 ce cece nee e neces 127 1L 49 1 7Scale zoOmizv vu eet A etui 127 RES LE e EE 127 11 49 3 set smooth scroll do Z0OM 6 ccc cece eee 127 11 49 4 smooth scroll do zoom 0 0 cece ees 127 11 50 CNS Data Functions esses 127 11 50 1 handle cng data hle 128 11 50 2 handle cns data file with cell ooooooooooooo 128 LDL AmmGIF Bunctions csinsnmeedeB rep ca 128 11 51 1 open cif dictionary file selector dialog 128 11 52 SHELXL bunctiong eese 128 11 52 I xXead shelxcinsshllez ou peer pe oa aa a 128 11 52 2 write shelx ins file 0 0 0 c ccc ccc e eee 129 11 53 Validation bunctonsg ccc eee aee 129 11 53 1 d ference map peaks 0 0 0 cece eee eee eee 129 11 53 2 gln asn b factor outliers 00 0 cece ee eee 129 11 54 Ramachandran Plot Function
124. aw Screenshot gt Simple Note that in side by side stereo mode you only get the left hand image Chapter 3 General Features 10 3 6 Raster3D output Output suitable for use by Raster3D s render can be generated using the scripting function raster3d file name where file name is such as test r3d There is a keyboard key to generate this file run render and display the image Func tion key F8 You can also use the function render image which will create a file coot r3d from which render produces coot png This png file is displayed using ImageMagick s display program by default Use something like set coot png display program gqview to change that to different display program gqview in this case set coot png display program open would use Preview by default on Macintosh To change the widths of the bonds and density lines use for example set raster3d bond thickness 0 1 and set raster3d density thickness 0 01 Similarly for bones set raster3d bone thickness 0 05 To turn off the representations of the atoms spheres set renderer show atoms 0 3 7 Display Manager This is also known as Map and molecule coordinates display control Here you can select which maps and molecules you can see and how they are drawn The Display and Active are toggle buttons either depressed active or undepressed inactive The Display
125. backwards or forwards Recall that the chain id needs to be quoted i e use A not A Note that chain id is when the Cos have been built with Baton Mode in Coot 5 10 Backbone Torsion Angles It is possible to edit the backbone and w angles indirectly using an option in the Model Fit Refine s dialog Edit Backbone Torsions When clicked and an atom of a peptide is selected this produces a new dialog that offers Rotate Peptide which changes this residues v and Rotate Carbonyl which changes Click and drag across the button to rotate the moving atoms in the graphics window You should know of course that mak ing these modifications alter the w angles of more than one residue 5 11 Docking Sidechains Docking sidechains means adding sidechains to a model or fragment that has currently only poly Ala where the sequence assignment is unknown The algorithm is basically the 14 R M Esnouf Polyalanine Reconstruction from Ca Positions Using the Program CALPHA Can Aid Initial Phasing of Data by Molecular Replacement Procedures Acta Cryst D53 666 672 1997 15 T A Jones amp S Thirup Using known substructures in protein model building and crystallography EMBO J 5 819 822 1986 16 ang high resolution 17 ie there are severely misplaced atoms 18 as for Rotate Translate Zone Section Section 5 3 Rotate Translate Zone page 30 Chapter 5 Modelling and Building same as in Cowtan s Buccaneer
126. be make directory maybe dir Where dir is a string make a directory dir if it doesn t exist and return error code function If it can be created create the directory dir return the success status like mkdir mkdir Returns zero on success or 1 if an error occurred If dir already exists as a directory return 0 of course Chapter 11 Scripting Functions 11 3 2 set show paths in display manager set show paths in display manager i function Where 1 is an integer number Show Paths in Display Manager Some people don t like to see the full path names in the display manager here is the way to turn them off with an argument of 1 11 3 3 show paths in display manager state show paths in display manager state function return the internal state What is the internal flag Returns 1 for yes display paths 0 for not 11 3 4 add coordinates glob extension add coordinates glob extension ext function Where ext is a string add an extension to be treated as coordinate files 11 3 5 add data glob extension add data glob extension ex function Where ext is a string add an extension to be treated as data reflection files 11 3 6 add dictionary glob extension add dictionary glob extension ext function Where ext is a string add an extension to be treated as geometry dictionary files 11 3 7 add map glob extension add map glob extension ext function Where ext is a string add an extension to be treate
127. be set using either HID gt Scrollwheel gt Attach scroll wheel to which map and selecting a map number or clicking the Scroll radio button for the map in the Display Manager You can turn off the map contour level changing by the scroll wheel using set scroll by wheel mouse 0 the default is 1 on 2 7 Selecting Atoms Several Coot functions require the selecting of atoms to specify a residue range for exam ple Regularize Refine Section Section 5 1 Regularization and Real Space Refinement page 27 or Rigid Body Fit Zone Section Section 5 4 Rigid Body Refinement page 30 Select atoms with the Left mouse See also Picking Section Section 9 9 sec picking page 61 Use the scripting function quanta buttons to make the mouse functions more like other molecular graphics programs to which you may be more accustomed 2 8 Virtual Trackball You may not completely like the way the molecule is moved by the mouse movement To change this try HID gt Virtual Trackball gt Flat To do this from the scripting interface vt surface 1 If you do want screen z rotation screen z rotation you can either use Shift Right Mouse Drag or set the Virtual Trackball to Spherical Surface mode and move the mouse along the bottom edge of the screen 1 See also Section 2 9 more on zooming page 7 2 Mouse movement in Spherical Surface mode generates a component of often undesirable screen z rotation particularly noti
128. bject number colour line width function dash density from x1 from y1 from zl to_x2 to_y2 to_z2 Where e object number is an integer number e colour is a string e line width is an integer number e dash density is a number e from_x1 is a number e from_y1 is a number e Pom zl is a number Chapter 11 Scripting Functions 169 e o r2 is a number e to_y2 is a number e to_z2 is a number add a dashed line to generic object object number dash_density is number of dashes per Angstrom 11 92 4 to generic object add point to generic object add point object number colour point width function from x1 from vi from_z1 Where e object number is an integer number e colour is a string point width is an integer number e from x1 is a number e from_y1 is a number e Pom zl is a number add point to generic object object number 11 92 5 to generic object add arc to generic object add arc object number colour point width function from angle to angle start point x start point y start point z start dir x start dir y start_dir_z normal_x1 normal y1 normal zl Where e object number is an integer number e colour is a string e poini width is an integer number e from angle is a number e to_angle is a number e start_point_x is a number e start_point_y is a number e start_point_z is a number e start_dir_x is a number e start_dir_y is a number e start_dir_z is a number e normal x is a number e normal
129. ble stranded is presented The interface may not gracefully handle uracils in DNA thymines in RNA or B form RNA 5 28 Merge Molecules This dialog can be found under Calculate in the main menubar This is typically used to add molecule fragments or residues that are in one molecule to the working coordinates 5 29 Temperature Factor for New Atoms The default temperature factor for new atoms is 30 0 This can be changed by the following set default temperature factor for new atoms 50 0 P including sulfate or phosphate ions in such a case it is probably useful to do a Rigid Body Fit Zone on that new residue 36 But you don t want those things anyway right 37 For example after a ligand search has been performed Chapter 5 Modelling and Building 5 30 Applying NCS Edits Let s imagine that you have 3 fold NCS You have molecule A as your master molecule and you make edits to that molecule Now you want to apply the edits that you made to A the NCS master chain ID to the B and C molecules i e you want the B and C molecules to be rotated translated versions of the A molecule How is that done There are now guis to NCS command to help you out under Extensions However for completeness here are the scripting versions copy from ncs master to others imol master chain id If you have only a range of residues rather than a whole chain to replace copy residue range
130. bonds colour map rotation set molecule bonds colour map rotation imol theta function Where e imolis an integer number e theta is a number set the colour map rotation for molecule number imol theta is in degrees 11 26 3 get molecule bonds colour map rotation get molecule bonds colour map rotation imol function Where mol is an integer number Get the colour map rotation for molecule number imol 11 27 Display Functions Chapter 11 Scripting Functions 11 27 1 set graphics window size set graphics window size x_size y_size Where e r size is an integer number e y_size is an integer number set the window size 11 27 2 set graphics window position set graphics window position x pos y pos Where e r pos is an integer number e y_pos is an integer number set the window position 11 27 3 graphics draw graphics draw draw a frame 11 27 4 zalman stereo mode zalman stereo mode try to turn on Zalman stereo mode 11 27 5 hardware stereo mode hardware stereo mode try to turn on stereo mode 11 27 6 stereo mode state Stereo mode state what is the stero state Returns 1 for in hardware stereo 2 for side by side stereo else return 0 11 27 7 mono mode mono mode try to turn on mono mode 11 27 8 side by side stereo mode side by side stereo mode use wall eye mode Where use wall ee mode is an integer number turn on side bye side stereo mode 104 function function function fun
131. buttons control whether a molecule or map is drawn and the Active button controls if the molecule is clickable i e if the molecule s atoms can be labeled The Scroll radio buttons sets which map is has its contour level changed by scrolling the mouse scroll wheel By default the path names of the files are not displayed in the Display Manager To turn them on set show paths in display manager 1 If you pull across the horizontal scrollbar in a Molecule view you will see the Render as menu You can use this to change between normal Bonds Colour by Atom Bonds Colour by Chain and Co representation There is also available No Waters and Ca ligands representations S Povray support is only semi working there is a problem with the orientation of the image 4 to a limited extent 5 the substantial majority of the time you will want your the buttons to be both either depressed or undepressed rarely one but not the other Chapter 3 General Features 11 3 8 The Modelling Toolbar You might not want to have the right hand side vertical toolbar that contains icons for some modelling operations displayed hide modelling toolbar to bring it back again show modelling toolbar 3 9 The file selector 3 9 1 File name Filtering The Filter button in the fileselection filters the filenames according to extension For coordinates files the extensions are pdb brk mmcif
132. bviously enough been added to aid debugging Most of them should have been cleaned up before release but as Coot is constantly being developed a few may slip through Just ignore them 21 22 23 compared to some other one prompted by changing the contour level i e the terminal in which you started Coot Chapter 4 Coordinate Related Features 18 4 Coordinate Related Features 4 1 Reading coordinates The format of coordinates that can be read by coot is either PDB or mmCIF To read coordinates choose File gt Read Coordinates from the menu bar Immediately after the coordinates have been read the view is by default recentred to the centre of this new molecule and the molecule is displayed The recentring of the view after the coordinates have been read can be turned off by unclicking the Recentre radio button To disable the recentring of the view on reading a coordinates file via scripting use set recentre on read pdb 0 However when reading a coordinates file from a script it is just as good if not better to use handle read draw molecule with recentre filename 0 the additional O means don t recentre And that affects just the reading of filename and not subsequent files Note that as of version 0 6 2 Coot can read MDL mol mol2 files the atom names are not unique of course but at least you can see the coordinates 4 1 1 A Note on Space Groups Names Coot uses the space group on the CRYST1 lin
133. ceable when the mouse is at the edge of the screen 5 vt surface 0 to turn it back to Spherical mode Chapter 2 Mousing and Keyboarding T 2 9 More on Zooming The function quanta like zoom adds the ability to zoom the view using just Shift Mouse movement There is also a Zoom slider Draw gt Zoom for those without a right mouse button this is off by default because I find it annoying Chapter 3 General Features 8 3 General Features The map fitting and model building tools can be accessed by using Calculate gt Model Fit Refine Many functions have tooltips describing the particular features and are documented in Chapter Chapter 5 Modelling and Building page 27 F5 posts the Model Fit Refine dialog F6 posts the Go To Atom Window F7 posts the Display Control Window 3 1 Version number The version number of Coot can be found at the top of the About window Help gt About This will return the version of coot coot version There is also a script function to return the version of coot coot version 3 2 Antialiasing The built in antialiasing for what it s worth can be enabled using set do anti aliasing 1 The default is O off This can also be activated using Edit Preferences gt Others gt Antialiasing gt Yes If you have an nVidia graphics card external antialiasing can be actived setting the environment variable __GL_FSAA_MODE For me a setting of 5 w
134. cedure procedure procedure procedure procedure procedure procedure procedure procedure procedure procedure procedure procedure procedure 0 1 2 e g Chapter 13 Scheme Scripting Functions 203 shell command to string cmd procedure code from thi ttn at mingle glug org gt run command and put the output into a string and return it c f run command strings shell command to file with data cmd file name data list procedure run cmd putting output to file name and reading commands data from the list of strings data list command in path f procedure Is the command f in the path return t or f Thank you for this rixed at happyleptic org command in path or absolute cmd procedure Return t or f goosh command cmd args data list log file name screen output also procedure Where cmd is e g refmac args is list HKLIN thing mtz log file name is refmac log data list is list HEAD END Return the exist status e g O or 1 goosh command with file input cmd args input file log file name procedure run commands from an input file run command strings cmd args data list procedure Return the strings screen output of cmd or f if command was not found close float xl x2 procedure Crude test to see of 2 floats are the same more or less Used in a greg test after setting the atom position strip spaces str procedure if passed a string return a
135. clear backups maybe So if you wanted to clear out everything more than 1 day old every time without Coot asking you about it define clear out backup run n days 0 define clear out backup old days 1 define clear backups maybe delete coot backup files delete coot real exit 0 9 5 Getting out of Translate Mode If you get stuck in translate mode in the GL canvas i e mouse does not rotate the view as you would expect simply press and release the Ctrl key to return to rotate mode 9 6 Getting out of Continuous Rotation Mode The keyboard I key toggles the continuous rotation mode The menu item Draw gt Spin View On Off does the same thing 9 7 Getting out of Label Atom Only Mode Similarly if you are stuck in a mode where the Model Fit Refine buttons don t work the atoms are not selected only the atom gets labelled press and release the Shift key 9 8 Button Labels Button labels ending in mean that a new dialog will pop up when this button is pressed 9 9 Picking Note that left mouse in the graphics window is used for both atom picking and rotating the view so try not to click over an atom when trying to rotate the view when in atom selection mode Chapter 9 Hints and Usage Tips 9 10 Resizing View Click and drag using right mouse up and down or left and right to zoom in and out 9 11 Scroll wheel To change the map to which the scroll whe
136. closeness function do positive level flag do negative level flag Where e imol is an integer number e imol_coords is an integer number e level is a number e maz_closeness is a number e do positive level flag is an integer number e do negative level flag is an integer number generate a list of difference map peaks peaks within max closeness 2 0 A typically of a larger peak are not listed 11 53 2 gln asn b factor outliers gln asn b factor outliers imol function Where mol is an integer number Make a gui for GLN adn ASN B factor outiers compairing the O and N temperatur factors difference to the distribution of temperature factors from the other atoms 11 54 Ramachandran Plot Functions 11 54 1 do ramachandran plot do ramachandran plot imol function Where mol is an integer number Ramachandran plot for molecule number imol 11 54 2 set kleywegt plot n diffs set kleywegt plot n diffs n diffs function Where n_diffs is an integer number set the number of biggest difference arrows on the Kleywegt plot Chapter 11 Scripting Functions 130 11 54 3 set ramachandran plot contour levels set ramachandran plot contour levels level prefered level allowed function Where e level prefered is a number e level allowed is a number set the contour levels for theremachandran plot default values are 0 02 prefered 0 002 allowed 11 54 4 set ramachandran plot background block size set ramacha
137. colour map rotation i e the hue change for the symmetry atoms of molecule number imol return state 0 for off state 1 for on 11 21 9 has unit cell state has unit cell state imol function Where mol is an integer number molecule number imol has a unit cell Returns 1 on yes it has a cell 0 for no 11 21 10 undo symmetry view undo symmetry view function Undo symmetry view Translate back to main molecule from this symmetry position 11 21 11 first molecule with symmetry displayed first molecule with symmetry displayed function return the molecule number Returns 1 if there is no molecule with symmetry displayed 11 21 12 save symmetry coords save symmetry coords imol filename symop_no shift a shift_b shift_c function pre shift to origin na pre_shift_to_origin_nb pre shift to origin nc Where e imol is an integer number e filename is a string e symop no is an integer number e shift_a is an integer number e shift_b is an integer number e shifi c is an integer number Chapter 11 Scripting Functions e pre_shift_to_origin_na is an integer number e pre_shift_to_origin_nb is an integer number e pre_shift_to_origin_nc is an integer number save the symmetry coordinates of molecule number imol to filename Allow a shift of the coordinates to the origin before symmetry expansion is apllied this is how symmetry works in Coot internals 11 21 13 new molecule by symmetry new molecule by symme
138. cript on exit either pdb filename for pdb coordinates file coords filename for SHELX ins res and CIF files data filename for mtz phs or mmCIF data file auto filename for auto reading mtz files mtz file has the default labels FWT PHWT map filename for a map currently CCP4 format only dictionary filename read in a cif monomer dictionary help print command line options stereo start up in hardware stereo mode version print the version of coot and exit code accession code on starting Coot get the pdb file and mtz file if it exists from the EDS no guano don t leave Coot droppings ie don t write state and history files on exit side by side start in side by side stereo mode update self command line mode to update the coot to the latest pre release on the server python an argument with no parameters used to tell Coot that the c arguments should be process as python rather than as scheme small screen start with smaller icons and font to fit on small screen displays zalman stereo start in Zalman stereo mode Chapter 1 Introduction 4 So for example one might use e coot pdb post refinement pdb auto refmac 2 mtz dictionary lig cif 1 7 Web Page Coot has a web page e http www biop ox ac uk coot There you can read more about the CCP4 molecular graphics project in general and other projects which are important for Coot 1 8 Crash Coot might crash on you it sh
139. cripting interface is and therefore most interesting 5 or the water should be more properly modelled as anistrotropic or a split partial site Chapter 7 Validation 57 check waters by difference map imol coords imol diff map where imol coords is the molecule number of the coordinates that contain the waters to be checked imol diff map is the molecule number of the difference map it must be a difference map not an ordinary map This difference map must have been calculated using the waters So there is no point in doing this check immediately after Find Waters You will need to run Refmac or some other refinement first first 7 7 Molprobity Tools Interface The molprobity tools probe and reduce have been interfaced into Coot currently the interface is not as slick as it might be However the tools are useful and can be used in the following way first we need to tell Coot where to find the relevant executables typically you would add the following lines to you coot file define probe command path to probe executable define reduce command path to reduce executable now the probe hydrogens and probe dots can be generated using Validate gt Probe Clashes or in the Scripting Window probe imol where imol is the molecule number of coordinates to be probed A new molecule with Hydrogens is created by reduce and read in By default Coot creates a new molecule for
140. ction function function function function Chapter 11 Scripting Functions 11 27 9 set hardware stereo angle factor set hardware stereo angle factor f Where f is a number how much should the eyes be separated in stereo mode 11 27 10 hardware stereo angle factor state hardware stereo angle factor state return the hardware stereo angle factor 11 27 11 set model fit refine dialog position set model fit refine dialog position x_pos y pos Where e r pos is an integer number e y_pos is an integer number set position of Model Fit Refine dialog 11 27 12 set display control dialog position set display control dialog position x pos y pos Where e r pos is an integer number e y_pos is an integer number set position of Display Control dialog 11 27 13 set go to atom window position set go to atom window position x pos y_pos Where e r pos is an integer number e y_pos is an integer number set position of Go To Atom dialog 11 27 14 set delete dialog position set delete dialog position x pos y_pos Where e r pos is an integer number e y_pos is an integer number set position of Delete dialog 105 function function function function function function Chapter 11 Scripting Functions 11 27 15 set rotate translate dialog position set rotate translate dialog position x pos y_pos Where e r pos is an integer number e y_pos is an integer number set posit
141. ction D Biological Crystallography 60 2240 2249 Please also cite the primary literature for the received structures 1 2 What is Coot Coot is a molecular graphics application Its primary focus is crystallographic macromolec ular model building and manipulation rather than representation i e more like Frodo than Rasmol Having said that Coot can work with small molecule SHELXL and electron mi croscopy data be used for homology modelling make passably pretty pictures and display NMR structures Coot is Free Software You can give it away If you don t like the way it behaves you can fix it yourself 1 3 What Coot is Not Coot is not e CCP4 s official Molecular Graphics program 1 The official CCP4 graphics program which contains parts of Coot and Coot contains parts of CCP4MG CCP4MG is under the direct control of Liz Potterton and Stuart McNicholas Chapter 1 Introduction 2 a program to do refinement a protein crystallographic suite 1 4 Hardware Requirements The code is designed to be portable to any Unix like operating system Coot certainly runs on SGI IRIX64 RedHat Linux of various sorts SuSe Linux and MacOS X 10 2 The sgi Coot binaries should also work on IRIX If you want to port to some other operating system you are welcome Note that your task will be eased by using GNU GCC to compile the programs components 1 4 1 Mouse Coot works best with a 3 button mouse and works be
142. ctive residue triple procedure refine active residue triple manual refine residues side residue offset procedure For just one this residue side residue offset is 0 pepflip active residue procedure Pepflip the active residue needs a key binding auto fit rotamer active residue procedure Auto fit rotamer on active residues add extra restraints to other molecule imol chain id procedure resno range start resno range end atom sel type imol ref Restrain the atoms in imol in give range selection to corresponding atoms in imol ref atom sel type is either all main chain or ca 13 24 refmac refmac exe procedure This is the default refmac version it is presumed to be in the path It can be overridden using a re definition either at the scripting interface or in one s coot file E g define refmac exec y programs xtal refmac latest bin refmac5 3 dec 2004 refmac extra params procedure Set this to a list of parameter strings If refmac extra params is a list of strings it is used in preference to the refmac extra params file should it exist e g set refmac extra params list WEIGHT 0 2 NCYC 10 REFI BREF ISO REFI METH CGMAT REFI TYPE REST RESO 20 1 64 run refmac by filename pdb in filename pdb out filename procedure mtz in filename mtz out filename extra cif lib filename imol refmac count swap map colours post refmac imol mtz molecule show diff map flag phase combine flag phib fom pa
143. d If you want coot to display symmetry coordinates without having to use the gui add to your coot the following set show symmetry master 1 The symmetry can be represented as Cas This along with representation of the molecule as Cas Section Section 3 7 Display Manager page 10 allow the production of a packing diagram using thermal ellipsoids o in the case of isotropic atoms ellipsoids are spherical of course 19 symmetry labels are in pale blue and also provide the symmetry operator number and the translations along the a b and c axes Chapter 4 Coordinate Related Features 23 4 11 1 Missing symmetry Sometimes rarely coot misses symmetry related molecules that should be displayed In that case you need to expand the shift search the default is 1 set symmetry shift search size 2 This is a hack until the symmetry search algorithm is improved 4 12 Sequence View The protein is represented by one letter codes and coloured according to secondary structure These one letter codes are active if you click on them they will change the centre of the graphics window in much the same way as clicking on a residue in the Ramachandran plot 4 13 Print Sequence The single letter code of the imo1th molecule is written out to the console in FASTA format Use can use this to cut and paste into other applications print sequence imol 4 14 Environment Distances Environment distances are tu
144. d then that is the map that has its contour level changed no matter what the scroll wheel is attached to in the menu The level of the electron density is displayed in the top right hand corner of the OpenGL canvas Use keyboard or to change the contour level if you don t have a scroll wheel DH If you are creating your map from an MTZ file you can choose to click on the is difference map button on the Column Label selection widget after a data set filename has been selected then this map will be displayed in 2 colours corresponding to and the map contour level If you read in a map and it is a difference map then there is a checkbutton to tell Coot that If you want to tell Coot that a map is a difference map after it has been read use set map is difference map imol where imol is the molecule number By default the change of the contour level is determined from the sigma of the map You can change this in the map properties dialog or by using the scripting function set contour by sigma step by mol step on off imol where step is the difference in sigma from one level to the next typically 0 2 on off is either 0 sigma stepping off or 1 sigma stepping on 2 like I don t on my Mac Chapter 6 Map Related Features 50 By default the map radius is 10 The default increment to the electron density depends on whether or not this is a difference map 0 05 e A3 for a 2Fo Fc style map and 0 005
145. d as geometry map files 11 3 8 remove coordinates glob extension remove coordinates glob extension ext function Where ext is a string remove an extension to be treated as coordinate files 11 3 9 remove data glob extension remove data glob extension ext function Where ext is a string remove an extension to be treated as data reflection files Chapter 11 Scripting Functions 11 3 10 remove dictionary glob extension remove dictionary glob extension ext Where ext is a string remove an extension to be treated as geometry dictionary files 11 3 11 remove map glob extension remove map glob extension ext Where ext is a string remove an extension to be treated as geometry map files 11 3 12 set sticky sort by date set sticky sort by date sort files in the file selection by date some people like to have their files sorted by date by default 11 3 13 unset sticky sort by date unset sticky sort by date do not sort files in the file selection by date removes the sorting of files by date 11 3 14 set filter fileselection filenames set filter fileselection filenames istate Where istate is an integer number on opening a file selection dialog pre filter the files set to 1 to pre filter 0 off non pre filtering is the default 11 3 15 filter fileselection filenames state filter fileselection filenames state return the state of the above variable 11 3 16 file type coords file type coords file name Where file n
146. d cif dictionary filename and add this to your coot file this may be the preferred method if you want to read the file on more than one occasion Note the dictionary also provides the description of the ligand s torsions 5 1 2 Sphere Refinement Sphere refinement selects residues within a certain distance of the residue at the centre of the screen and includes them for real space refinement In this way one can select residues that are not in a linear range This technique is useful for refining disulfide bonds and glycosidic linkages To enable sphere refinement Right mouse in the vertical toolbutton menu Manage buttons gt Tick Sphere Refine gt Apply You will need a python enabled Coot to do this The following adds a key binding Shift R that refines resides that are within 3 5 of the residue at the centre of the screen define sphere refine radius 3 5 add key binding Refine residues in a sphere R lambda using active atom And a few extras such as phosphate Chapter 5 Modelling and Building 29 let rc spec list aa chain id aa res no aa ins code 1s residues near residue aa imol rc spec sphere refine radius refine residues aa imol cons rc spec 1s 5 1 3 Refining Specific Residues You can specify the residues that you want to refine without using a linear or sphere selection usine refine residues For example refine residues O L 501 L 503 will
147. dary structure find secondary structure use helix helix length helix target function use_strand strand length strand target Where e use helir is an integer number e helix length is an integer number e helix target is an integer number e use strand is an integer number e strand length is an integer number e strand target is an integer number autobuild secondary structure Find secondary structure in the current map Add to a molecule called SecStruc create it if needed Returns the index of the new molecule 11 82 7 find secondary structure local find secondary structure local use helix helix length helix target function use strand strand length strand target radius Where e use helir is an integer number e helix length is an integer number e helix target is an integer number e use strand is an integer number e strand length is an integer number e strand target is an integer number e radius is a number autobuild secondary structure Find secondary structure local to current view in the current map Add to a molecule called SecStruc create it if needed Returns the index of the new molecule 11 83 Nucleotides 11 83 1 find nucleic acids local find nucleic acids local radius function Where radius is a number autobuild nucleic acid chains Find secondary structure local to current view in the current map Add to a molecule called NuclAcid create it if needed Returns the index of the new molecule
148. dist max 176 fle view set water dist max 176 flip active ligand suus 209 EL paid c udi dec SOM Ras 136 full atom spec to atom index 114 G generic buttons dialog s s 189 generic chooser and entry 189 generic chooser and file selector 189 220 generic chooser entry and file selector RETE 189 Seneric double entrg sess 187 generic interesting things 190 generic molecule chooser 190 generic multiple entries with check button uL TET 187 Beneric munber chooger 190 Beneric obiect clesr ooo 171 generic object has objects p 171 Seneric obiect Ander suus 170 Beneric obiect Anfo 0 eee 170 generic object is displayed p 170 generic object is displayed 194 generic object with name 194 generic objects gui 0 eee eee 194 generic objects gui wrapper 171 Beneric single entrg sess 187 get active map drag flag 85 PELTALOM caer ues a case at ado aas 204 get atom colour from mol no 174 get coords for accession code 118 get default bond thickness 138 Set drug via gikipedia sss 211 get ebi pdb iii idas A RR E 192 get electrostatic surface opacity 166 get file mtime 4 181 seek Ve ee bts 186 get first ncs master chain 206 get f
149. e 181 12 7 4 active residue ccc ccc cece nent en 181 12 725 elosest atom iva eh le eens 182 12 7 6 residues near residue sss 182 12 8 Refinement with specs sssssseeeesse a 182 12 8 1 rebne zone aitb Dulkreaidue apec acm s s snrsreusu 182 12 9 Water Chain Functions sseeeeeseeseeee ee 182 12 9 1 water cham Drom sbel Ans acm essre 183 12 9 2 water cham scm 00 c cece eee nnn 183 12 10 Spin Search Functions 0 000 cece eee eee eens 183 12 10 1 spin search wad eeii ae 183 NN protem dD 2 525 xs ed utes 183 12 11 1 protein db loops sssssseees ene eee ees 183 12 12 Coot s Hole implementation 0c eee eee eee 184 TOAD A A ee er Ee E Ate EERE ET 184 12 13 Drag and Drop bunctions cs 184 12 13 1 bhandle Jrag and drop atmng esena 184 12 14 Sectionless Dunctong 0 00 cece eee ees 184 12 14 1 ligand search make conformers ScmM ssuss sesse 184 13 Scheme Scripting Functions 185 13 1 redefbne Punctions 0 0 cence e 185 13 2 Jligand Oui ia sce cid nC A ir lee 185 13 3 get recent pdbe 00 ccc cece eee teen eee eee e eee 185 13 4 Tia A A Uh Menta et 186 13 5 user debne restraimts 0 00 cece cece eee eee eens 186 13 6 CNS2COOt 2 23 phen os Sat ie eee gU UE REI 186 13 7 groUp Settin gs 2 s ees A A eee ot 186 13 8 clear backtip rito e edie EH 186 13 9 quat conVerts isle EE te A EE 187 13 10 A A AA at 187 ISSUE EI A lb 187 xxii 13 12 gt H
150. e a gui to type functions in to start with handle smiles go tlc entry smiles entry procedure The callback from pressing the Go button in the smiles widget an interface to run libcheck smiles gui procedure smiles GUI generic single entry function label entry 1 default text procedure go button label handle go function Generic single entry widget Pass the hint labels of the entries and a function that gets called when user hits Go The handle go function accepts one argument that is the entry text when the go button is pressed generic double entry label 1 label 2 entry 1 default text procedure entry 2 default text check button label handle check button function go button label handle go function handle go function takes 3 arguments the third of which is the state of the check button if check button label not a string then we don t display or create even the check button If it is a string create a check button and add the callback handle check button function which takes as an argument the active state of the the checkbutton generic multiple entries with check button entry info list procedure check button info go button label handle go function generic double entry widget now with a check button OLD Chapter 13 Scheme Scripting Functions 188 pass a the hint labels of the entries and a function handle go function that gets called when user hits Go which takes two string aguments and the active st
151. e delete zero occ is 0 to remove the atoms and 1 to set their occupancy to zero There is a GUI interface for this feature under the Extensions menu item 6 19 Map Transformation If you want to transform a map you can do it thusly transform map imol rotation matrix trans point radius where rotation matrix is a 9 membered list of numbers for an orthogonal rotation matrix trans is a 3 membered list of numbers distances in Angst ms point is a 3 membered list of numbers centre point in ngst ms radius is a single number also in ngst ms This applies the rotation rotation matrix and a translation trans to a map fragment so that when the transformation is applied the centre of the new map is at point Example usage transform map2 100010001 00 1 rotation centre 10 which transforms map number 2 by a translation of 1A along the Z axis centred at the screen centre for 10 around that centre Here s a more real world example Let s say we want to tranform the density over the B molecule to a position over the A molecule First we do a LSQ transformation to get the rotation and translation that moves the B coordinates over the A coordinates In the terminal output we get 10 or set their occupancy to zero Chapter 6 Map Related Features 94 0 9707 0 2351 0 05033 0 04676 0 39 0 9196 0 2358 0 8903 0 3896 33 34 21 14 18 82 The centre of the A molecul
152. e eee 208 res spec ins code eee eee eee 209 res spec zres No coco 208 RE ius bos en ea posses ee 72 residue alt confs isis sss ess 208 residue atom z alt eonf oo 202 residue atom atom name oooooocooooo o 202 residue density fit scale factor 93 residue existS poene Rees 207 residue has hetatms ss T5 Function Index residue has hetatms sss 207 residue infon ccc ess er 181 residue range gui 6 cee eee eee 191 residue spec atom for centre 209 residue spec gt atom selection string 202 residue spec gt chain id 202 Tesidue Spec 2 ettring 192 residues matching criteria 208 Tesidues Heat Cesidue 00 182 residues with alt confs 208 resname from serial number 67 restore previous map colour 85 rigid body refine by residue ranges 201 rigid body refine zone 143 rotamer auto fit do post refine state 150 rotate about screen axis 205 rotate X sCene couvesnisbvertpi hea 131 rotate y sCene sc e 131 rotate z sCene i led lle Y ua 131 rotation cehtre ln il d Lips Is 202 run command strings 203 211 212 run download binary curl s 210 run gtk pending events sss 187 r n prosmart 2 it e 186 run refmac by filename 196 run refmac for p
153. e is an integer number set the state of show unit cell for the particular molecule number imol 1 for displayed 0 for undisplayed 11 25 Colour 11 25 1 set colour map rotation on read pdb set colour map rotation on read pdb f Where f is number set the hue change step on reading a new molecule 11 25 2 set colour map rotation on read pdb flag set colour map rotation on read pdb flag i Where i is an integer number shall the hue change step be used 11 25 3 set colour map rotation on read pdb c only flag set colour map rotation on read pdb c only flag i Where 1 is an integer number shall the colour map rotation apply only to C atoms 11 25 4 set colour by chain set colour by chain imol Where mol is an integer number colour molecule number imol by chain type 102 function function function function function function function Chapter 11 Scripting Functions 103 11 25 5 set colour by molecule set colour by molecule imol function Where mol is an integer number colour molecule number imol by molecule 11 25 6 set symmetry colour set symmetry colour rgb function Where e risa number e gisa number e bisa number set the symmetry colour base 11 26 Map colour 11 26 1 set colour map rotation for map set colour map rotation for map f function Where f is a number set the colour map rotation hue change for maps default for maps is 14 degrees 11 26 2 set molecule
154. e is at 58 456 5 65 11 108 So we do transform map 3 list 0 9707 0 2351 0 05033 0 04676 0 39 0 9196 0 2358 0 8903 0 3896 list 33 34 21 14 18 82 list 58 456 5 65 11 108 8 Which creates a map over the middle of the A molecule Note that using a too high radius can cause overlap problems so try with a small radius e g 5 0 if the resulting map looks problematic Alternatively instead of typing the whole matrix you can use a coordinates least squares fit to generate the matrix for you transform map using lsq matrix does just that Heres how to use it transform map using lsq matrix imol ref ref chain ref resno start ref resno end imol mov mov chain mov resno start mov resno end imol map about pt radius Hopefully the arguments are self explanatory ref refers to the reference molecule of course and about pt is a 3 number list such as is returned by rotation centre We can now export that map if we want 6 20 Export Map You can write out a map from Coot e g one from NCS averaging or masking or general transformation using the export map function export map imol filename e g export map 4 ncs averaged map Chapter 7 Validation 55 7 Validation The validation functions are still being added to from time to time In future there will be more functions particularly those that will interface to other programs 7 1 Ramachandran Plots Ramachandran plots are dynamic When you edit
155. e number imol to filename Return 0 on failure 1 on success 11 15 18 export map fragment export map fragment imolx y z radius filename function Where e imol is an integer number e risa number e y isa number e z isa number e radius is a number e filename is a string export a fragment of the map about x y z Chapter 11 Scripting Functions 11 15 19 difference map difference map imoll imol2 map scale function Where e imoll is an integer number e imol2 is an integer number e map scale is a number make a difference map taking map scale imap2 from imapl on the grid of imapl Return the new molecule number Return 1 on failure 11 16 Density Increment 11 16 1 set iso level increment set iso level increment val function Where val is a number set the contour scroll step in absolute e A3 for 2Fo Fc style maps to val The is only activated when scrolling by sigma is turned off 11 16 2 set diff map iso level increment set diff map iso level increment val function Where val is number set the contour scroll step for difference map in absolute e A3 to val The is only activated when scrolling by sigma is turned off 11 16 3 set map sampling rate set map sampling rate r function Where r is a number set the map sampling rate default 1 5 Set to something like 2 0 or 2 5 for more finely sampled maps Useful for baton building low resolution maps 11 16 4 get map sampling rate get m
156. e of the pdb file The space group should be one of the xHM symbols listed for example in the CCP4 dictionary file syminfo 1ib So for example R 3 2 H should be used in preference to H32 4 1 2 Read multiple coordinate files The reading multiple files using the GUI is not available at the moment However the following scripting functions are available read pdb all which reads all the pdb files in the current directory multi read pdb glob pattern dir which reads all the files matching g1ob pattern in directory dir Typical usage of this might be multi read pdb a pdb Alternatively you can specify the files to be opened on the command line when you start coot see Section Section 1 6 Command Line Arguments page 3 4 1 3 SHELX ins res files SHELX res and ins of course files can be read into Coot either using the GUI File Open Coordinates or by the scripting function read shelx ins file file name where file name is quoted such as thox ins Although Coot should be able to read any SHELX res file it may currently have trouble displaying the bonds for centro symmetric structures ShelxL atoms with negative PART numbers are given alternative configuration identifiers in lower case Chapter 4 Coordinate Related Features 19 To write a SHELX ins file write shelx ins file imol file name where imol is the number of the molecule you wish to export This will be a
157. e sorted by size the biggest one first with an index of 0 The output placed ligands files have a prefix best overall and are tagged by the cluster index and residue type of the best fit ligand in that site By default the top 10 sites are tested for ligands to increase this use set ligand n top ligands 20 5 20 1 Flexible Ligands If the Flexible checkbutton is activated coot will generate a number of variable con formations default 100 by rotating around the rotatable bonds torsions Each of these conformations will be fitted to each of the potential ligand sites in the map and the best one will be selected again if it passes the fitting criteria above Before you search for flexible ligands you must have read the mmCIF dictionary for that particular ligand residue type File gt Import CIF dictionary Use set ligand flexible ligand n samples n samples where n samples is the number of samples of flexibility made for each ligand Generally speaking The more the number of rotatable bonds the bigger this number should be By default the options to change these values are not in the GUI To enable these GUI options use the scripting function ligand expert 5 20 2 Adding Ligands to Model After successful ligand searching one may well want to add that displayed ligand to the current model the coordinates set that provided the map mask To do so use Merge Molecules Section Section 5 28 Merge Molecules
158. e state is an integer number make the map displayed undisplayed 0 for off 1 for on 11 38 3 set mol displayed set mol displayed imol state function Where e imolis an integer number e state is an integer number make the coordinates molecule displayed undisplayed 0 for off 1 for on 11 38 4 set mol active set mol active imol state function Where e imolis an integer number e state is an integer number make the coordinates molecule active inactve clickable 0 for off 1 for on 11 38 5 mol is displayed mol is displayed imol function Where mol is an integer number return the display state of molecule number imol Returns 1 for on 0 for off 11 38 6 mol is active mol is active imol function Where mol is an integer number return the active state of molecule number imol Returns 1 for on 0 for off 11 38 7 map is displayed map is displayed imol function Where mol is an integer number return the display state of molecule number imol Returns 1 for on 0 for off Chapter 11 Scripting Functions 116 11 38 8 set all maps displayed set all maps displayed on or off function Where on_or_off is an integer number if on or off is 0 turn off all maps displayed for other values of on_or_off turn on all maps 11 38 9 set all models displayed and active set all models displayed and active on or off function Where on_or_off is an integer number if on or off is 0 turn off all models displayed and
159. e view is orthographic i e the back is the same size as the front The default clipping is about right for viewing coordinate data but is often a little too thick for viewing electron density It is easily changed see Section Section 3 16 Clipping Manipulation page 16 Depth cueing is linear and fixed on The graphics window can be resized but it has a minimum size of 400x400 pixels 3 4 1 Stereo Hardware Stereo is an option for Coot Draw gt Stereo gt Hardware Stereo gt OK side by side stereo is not an option The angle between the stereo pairs the stereo separation can be changed to suit your personal tastes using set hardware stereo angle factor angle factor where angle factor would typically be between 1 0 and 2 0 3 4 2 Pick Cursor When asked to pick a residue or atom the cursor changes from the normal arrow shape to a pick cursor Sometimes it is difficult to see the default pick cursor so you can change it using the function set pick cursor index i where i is an integer less than 256 The cursors can be viewed using an external X program xfd fn cursor 3 4 3 Origin Marker A yellow box called the origin marker marks the origin It can be removed using set show origin marker 0 Its state can be queried like this show origin marker state which returns an number 0 if it is not displayed 1 if it is 3 5 Screenshot A simple screenshot image dump can be made using Dr
160. eading Bug Unfortunately there is a bug in map reading If the map is not a bona fide CCP4 map then coot will crash Sorry A fix is in the works but it s complicated That s why maps are limited to the extension ext and map to make it less likely a non CCP4 map is read 6 2 Create a Map From MTZ mmCIF and phs data use File gt Open MTZ CIF or phs You can then choose the M TZ columns for the Fourier synthesis The button Expert mode also adds to the options any anomalous columns you may have in the MTZ file a 90 degree phase shift will be applied It also provides the option to apply resolution limits From a CCP4 map use File gt Read Map After being generated read the map is immediately contoured and centred on the current rotation centre 6 2 1 Auto read MTZ file This function allows Coot to read an MTZ file and make a map directly without going through the column selection procedure The default column labels for auto reading are FWT and PHWT for the 2Fo Fc style map DELFWT and PHDELWT for the difference map You can change the column labels that Coot uses for auto reading here is an example of how to do that set auto read column labels 2FOFCWT PHIWT 0 set auto read column labels FOFCWT DELPHIWT 1 By default the difference map is created in auto reading the MTZ file If you don t want a difference map you can use the function set auto read do difference map too 0 6
161. earch make conformers scm 184 list Of sStrings wi el drm ta RR 202 load all scheme seen 199 load annotations eee 210 JLoad default seguence 210 lsq improve 2 scr ea ho LAE 176 RE e E EE 214 1sq match type symbol gt number 213 EE AA eden EE 193 M EE 213 make and draw map eee 89 make and draw map with refmac params 89 make and draw map with reso with refmac params erica sete ehh A 90 make and draw patterson sess 178 make back p ussstelxei re 81 make ball and etick 141 make difference map gui sss 190 make directorg magbe rro 64 Function Index make dynamically transformed ncs maps 157 make gdb script isses 212 MARE er UPPER DOM 212 make latest version url 210 make socket listener maybe 167 manage column selector ss 67 manual ncs ghosts oooococcococcccooc 191 manual refine residues sns 196 map colour componentsS sess 179 map from mtz by calc phases 84 map from mtz by refmac calc phases 84 map is displayed op bd seein 115 map Line vidtbh etate sues 89 map mask atom Cadius oo 154 map molecule chooser gui 189 map molecule list eee 202 mask map by molecule eee eee 153 match ligand atom names 135 matrix quaternion sess 187 205 patrik stato ii e OIX Reds 120
162. eate a dummy atom at the pointer position Use an argument of O to revert to using the atom type selection pop up on a button press The atoms are added to a new molecule called Pointer Atoms They should be saved and merged with your coordinates outside of Coot 5 26 Place Helix The idea is to place a helix more or less here the screen centre by fitting to the electron density map The algorithm is straightforward First we move to the local centre of density then examine the density for characteristic directions and fit ideal helices of length 20 residues to these directions The helix is then extended if possible by checking the fit to the map of residues added in ideal helix conformation and chopped back if not If the fit is successful the helix is created in a new molecule called Helix If the fit is not successful there is instead a message added to the status bar You can build the majority of a helical protein in a few minutes using this method you will of course have to assemble the helices and assign residue numbers and sequence later This is available as a scripting function place helix here and in the GUI in the Other Modelling Tools dialog 5 27 Building Ideal DNA and RNA The interface to building ideal polynucleotides can be found by pressing the Ideal RNA DNA button on the Other Modelling Tools dialog For a given sequence a choice of DNA or RNA A or B form single or dou
163. ed by a simple water So for example sulfates ligands mis placed sidechains or unbuilt terminal residues might appear as blobs The blobs are in order the biggest at the top 7 5 Difference Map Peaks This is one of the fastest ways to validate a model and its data presuming that the difference map comes from a post refinement mFo DFc map It highlights regions where the model and the data do not agree Lesser peaks within a certain distance by default 2 0 of a large peak are not shown This cuts down on the number of times one is navigated to a particular region because of ripple or other noise peaks around a central peak This value can be queried difference map peaks max closeness and adjusted set difference map peaks max closeness 0 1 7 6 Check Waters by Difference Map Sometimes waters can be misplaced taking the place of sidechains or ligands or crystal lization agents such as phosphate for example In such cases the variance of the difference map can be used to identify these problems This function is also useful to check anomalous maps Often waters are placed in density that is really a something else perhaps a cation anion sulphate or a ligand If such an atom diffracts anomalously this can be identified and corrected By default the waters with a map variance greater than 3 50 are listed One can be more rigorous by using a lower cut off set check waters by difference map sigma level 3 0 The s
164. ee ae VE 91 set map sampling rate ess 87 set map sharpening scale limit 173 set match element eee 213 Set matrix EE 120 225 set max skeleton search depth 110 set model fit refine dialog position 105 set model fit refine place atom at pointer WADE Use i jd ela veio eheu 81 set model fit refine rotate translate zone E DEE 81 set model toolbar docked position 79 St llen dE a ri 115 set mol displayed sees 115 set molecule bonds colour map rotation 103 Set m0olecule name 0 eee 71 set monomer restraints esses 180 set mutate auto fit do post refine 150 set ncs ghost bond thickness 157 set ncs homology level 159 set nomenclature errors on read 125 Set Dlck cureor Jnder sees 80 set prefer python sriti arire cece cece 64 set ramachandran plot background block size D 130 set ramachandran plot contour levels 130 set ramachandran plot dialog position 106 set raster3d atom radius 155 set raster3d bond thickness 155 set raster3d bone thickness 155 set raster3d density thickness 155 set raster3d shadows enabled 155 set raster3d water sphere 155 set refine auto range step 120 set refine max residues 120 set refine ramachandran angles
165. el is attached use the scroll check button in the Display Manager or use HID gt Scrollwheel gt Attach Scrollwheel to which map 9 12 Slow Computer Configuration Several of the parameters of Coot are chosen because they are reasonable on my middle ground development machine However these parameters can be tweaked so that slower computers perform better set smooth scroll steps 4 default 8 set smooth scroll limit 30 Angstroms set residue selection flash frames number 3 set skeleton box size 20 0 A default 40 set active map drag flag 0 turn off recontouring every step set idle function rotate angle 1 5 continuous spin speed Chapter 10 Other Programs 10 Other Programs 10 1 findligand findligand is a stand alone command line program that uses the libraries of Coot findligand provides a number of command line arguments for increased flexibility e pdbin pdb in filename where pdb in filename is the protein typically e hklin mtz filename e f f col label e phi phi col label e clusters nclust where nclust is the number of density clusters potential ligand sites to search for e sigma sigma level where sigma level the density level in sigma above which the map is searched for ligands e fit fraction frac where frac is the minimum fraction of atoms in density allowed after fit default 0 75 e flexible means use torsional conformation ligand search e samples nsamples nsampl
166. ement immediate replacement state refinement immediate replacement state function query the state of the immediate replacement mode 11 43 7 set residue selection flash frames number set residue selection flash frames number i function Where i is an integer number set the number of frames for which the selected residue range flashes On fast computers this can be set to higher than the default for more aesthetic appeal 11 43 8 accept regularizement accept regularizement function accept the new positions of the regularized or refined residues If you are scripting refinement and or regularization this is the function that you need to call after refine zone or regularize zone Chapter 11 Scripting Functions 120 11 43 9 set refine with torsion restraints set refine with torsion restraints istate function Where istate is an integer number turn on or off torsion restraints Pass with istate 1 for on istate 0 for off 11 43 10 refine with torsion restraints state refine with torsion restraints state function return the state of above 11 43 11 set matrix set matrix f function Where f is number set the relative weight of the geometric terms to the map terms The default is 60 The higher the number the more weight that is given to the map terms but the resulting chi squared values are higher This will be needed for maps generated from data not on or close to the absolute scale or maps that have been scaled for exam
167. er 211 Coot Versione r s 24 bet Cae ais 70 cootaneer AE 190 copy chain hor gelo nales i4 159 copy from ncs master to others 159 copy molecule noie ii ed 69 copy residue range sees 75 copy residue range from ncs master to eg cing Tubi ee et ale RLAS 160 create pointer atom molecule maybe 151 D darken maps oii hs ened ed ence da 206 219 data resolution csse 86 dbzmainch in v ake oda 147 decrease coot tip number 212 default new atoms b factor 108 delete all extra restraints 124 delete all sequences from molecule 165 delete atom ug Ee Ae Ae PELO 146 delete atom by active residue 209 delete checked waters baddies 154 delete coot backup files 186 delete extra restraints for residue 124 delete hydrogens 0 cece cece 147 delete residue eee 145 delete residue hydrogens 146 delete residue range suus 145 delete residue sidechain 146 delete residue with full spec 146 delete section texi fileS 211 delete sequence by chain id 166 delete sidechain range 213 density at point lbe eil d 93 d ialog bosz of buttons ss 190 dialog box of buttons with async ligands Wod Xuwco di wem e Mere LA EUN PU Pr 185 dialog box of buttons with check button EE 190 dialog box of pair
168. er e chain id is a string e res no is an integer number e ins_code is a string e new_residue_name is a string set lots of atom attributes at once by passing the rebonding and redrawing of the above 2 functions 11 32 Skeletonization Interface 11 32 1 skeletonize map Skeletonize map prune_flag imol function Where e prune flag is an integer number Chapter 11 Scripting Functions 110 e mol is an integer number skeletonize molecule number imol the prune flag should almost always be 0 11 32 2 unskeletonize map unskeletonize map imol function Where mol is an integer number undisplay the skeleton on molecule number imol 11 32 3 set max skeleton search depth set max skeleton search depth v function Where v is an integer number set the skeleton search depth used in baton building For high resolution maps you need to search deeper down the skeleton tree This limit needs to be increased to 20 or so for high res maps it is 10 by default 11 32 4 set skeleton box size set skeleton box size f function Where f is number the box size in Angstroms for which the skeleton is displayed 11 33 Read Maps 11 33 1 handle read ccp4 map handle read ccp4 map filename is diff map flag function Where e filename is a string e is diff map flag is an integer number read a CCP4 map or a CNS map despite the name 11 34 Save Coordinates 11 34 1 save coordinates save coordinates imol filename fu
169. erates a c4 map and a difference map Coot creates a time stamped ins file and a time stamped sym link to the hk1 file in the coot shelxl directory Please note that the output ins file will not be particularly useful and thus shelxl will fail if the input file was not in SHELX ins format There is a GUI for this operation under the Extensions menu item 5 33 Clear Pending Picks Sometimes one can click on a button unintentionally This button is there for such a case It clears the expectation of an atom pick This works not only for modelling functions but also geometry functions such as Distance and Angle 5 34 Delete Single atoms or residues can be deleted from the molecule using Delete from the Model Fit Refine dialog Pressing this button results in a new dialog with the options of Residue the default Atom and Hydrogen Atoms Now click on an atom in the graphics the deleted object will be the whole residue of the atom if Residue was selected and just that atom if Atom was selected Note that if a residue has an alternative conformation then Delete Residue will delete only the conformation that matches that alternative conformation specifier of the clicked atom Only waters are deletable if the Water check button is active and waters are not deletable if the Residue Monomer check button is active This is to reduce mis clicking 20 such that Coot would subsequently ex
170. ere mol is an integer number set the molecule number imol to be marked as having unsaved changes 11 13 6 have unsaved changes p have unsaved changes p imol function Where mol is an integer number does molecule number imol have unsaved changes Returns 1 on bad imol 0 on no unsaved changes 1 on has unsaved changes 11 13 7 set undo molecule set undo molecule imol function Where mol is an integer number set the molecule to which undo operations are done to molecule number imol 11 13 8 show set undo molecule chooser show set undo molecule chooser function show the Undo Molecule chooser i e choose the molecule to which the Undo button applies Chapter 11 Scripting Functions 11 13 9 set unpathed backup file names set unpathed backup file names state function Where state is an integer number set the state for adding paths to backup file names by default directories names are added into the filename for backup with to mapping call this with state 1 to turn off directory names 11 13 10 unpathed backup file names state unpathed backup file names state function return the state for adding paths to backup file names 11 13 11 backup compress files state backup compress files state function return the state for compression of backup files 11 13 12 set backup compress files set backup compress files state function Where state is an integer number set if backup files will be compressed or not
171. ere is a GUI to control this too under Edit gt Bond Parameters 4 5 3 NCS Ghosts Coordinates It is occasionally useful when analysing non crystallographically related molecules to have images of the other related molecules appear matched onto the current coordinates It is important to understand that these ghosts are for displaying differences of NCS related molecules by structure superposition not displaying neighbouring NCS related molecules As you read in coordinates in Coot they are checked for NCS relationships and clicking on Edit gt Bond Parameters gt Show NCS Ghosts Yes gt Apply will create ghost copies of them over the reference chain Sometimes SSM does not provide a good or even useful matrix In that case we can specify the residue range ourselves and let the LSQ algorithm provide the matrix A gui dialog for this operation can be found under Extensions gt NCS gt NCS Ghosts by Residue Range The scripting function is used like this manual ncs ghosts imol resno start resno end ncs chain ids Typical usage manual ncs ghosts 0 1 10 list A B C note that in ncs chain ids the NCS master reference chain id goes first 2 they can be redisplayed using set draw hydrogens mol no 1 3 the reference chain is by default the first chain of that type in the coordinates file The reference master chain can be changed using the NCS Ghosts Control dialog Chap
172. es is the number of flexible conformation samples default 30 e dictionary cif dictionary name the file containing the CIF ligand dictionary description One uses findligand like this findligand various args ligand pdb file name s i e the example ligand pdb files that you wish to search for are given at the end of the command line Chapter 11 Scripting Functions 11 Scripting Functions 11 1 The Virtual Trackball 11 1 1 vt surface vt surface mode Where mode is an integer number How should the mouse move the view mode 1 for Flat mode 2 for Spherical Surface 11 1 2 vt surface status vt surface status return the mouse view status mode mode 1 for Flat mode 2 for Spherical Surface 11 2 Startup Functions 11 2 1 set prefer python set prefer python function function function tell coot that you prefer to run python scripts if when there is an option to do so 11 2 2 prefer python prefer python the python prefered mode function This is available so that the scripting functions know whether on not to put themselves onto in as menu items If you consider using this consider in preference use_gui_qm 2 which is used elsewhere to stop python functions adding to the gui when guile gtk functions have alread done so We should clean up this rather obscure interface at some stage return 1 for python is prefered 0 for not 11 3 File System Functions 11 3 1 make directory may
173. esidue By default this provides a choice of rotamer Section Section 5 12 Rotamers page 34 If there are not the correct main chain atoms a rotamer choice cannot be provided and Coot falls back to providing intermediate atoms The default occupancy for new atoms is 0 5 This can be changed by using use slider on the rotamer selection window or by using the scripting function set add alt conf new atoms occupancy 0 4 The remaining occupancy of the atoms after the new occupancy has been added is split amongst the atoms that existed in the residue before the split It is important therefore that the residues atoms have sane occupancies before adding an alternative conformation The default Split Type is to split the whole residue If you want the default to be to split a residue after and including the CA then add to your coot file set add alt conf split type number 0 Chapter 5 Modelling and Building 5 17 Mutation Mutations are available on a 1 by 1 basis using the graphics After selecting Mutate from the Model Fit Refine dialog click on an atom in the graphics A Residue Type window will now appear Select the new residue type you wish and the residue in the graphics is updated to the new residue type The initial position of the new rotamer is the a priori most likely rotamer Note that in interactive mode such as this a residue type match will not stop the mutation action occurring 5 17 1 M
174. esidue number residue type function immediate add Where e imolis an integer number e chain id is a string e residue number is an integer number e residue type is a string e immediate add is an integer number Add a terminal residue residue type can be auto and immediate add is recommended to be 1 return 0 on failure 1 on success 11 66 3 add terminal residue using phi psi add terminal residue using phi psi imol chain_id res_no function residue type phi psi Where e imol is an integer number e chain id is a string e res no is an integer number e residue type is a string e phi is a number Chapter 11 Scripting Functions e psi is a number Add a terminal residue using given phi and psi angles 11 66 4 set add terminal residue default residue type set add terminal residue default residue type type Where type is a string set the residue type of an added terminal residue 11 66 5 set add terminal residue do post refine set add terminal residue do post refine istat Where istat is an integer number set a flag to run refine zone on terminal residues after an addition 11 66 6 add terminal residue do post refine state add terminal residue do post refine state what is the value of the previous flag 11 67 Delete Residues 11 67 1 delete residue range delete residue range imol chain id resno_start end_resno Where e mol is an integer number e chain_id is a string e resno start is an integer number
175. esidues Again the length of the sequence must correspond to the residue range length Note also that this is a protein sequence not nucleic acid For mutation of nucleic acids use mutate nucleotide range imol chain id resno start resno end sequence 25 Note that selecting a residue type that matches the residue in the graphics will also result in a mutation 26 27 28 i e the current residue type matches the residue type to which you wish to mutate the residue e g after using Ca gt Mainchain i e the residue atoms will remain untouched Chapter 5 Modelling and Building 5 17 3 Mutating to a Non Standard Residue Sometimes one might like to model post translational or other such modifications How is that done if the new residue type is not one of the standard residue types There is a scripting function mutate by overlap imol chain id resno new three letter code This imports a model residue for the new residue type and overlays it on to the given residue by using graph matching to determine the equivalent atoms The GUI for this can be found under Extensions gt Modelling gt Replace Residue for this to work you need to be centred on the residue you wish to replace Note that if you are replacing are conventional protein residue with a modified form e g replacing a TYR with a phoso tyrosine or a LYS with an acetyl lysine you will need to make sure that the group of the resulting restraints is an L peptide
176. et esoteric depth cue esses 92 11 17 16 esoteric depth cue state kee eee eens 92 11 17 17 set swap difference map colours 2000 e eee 92 11 17 18 set map is difference map 0 e eee eee eee ee 92 11 17 19 another Jevel 2 00 cece cece een eee teenies 92 11 17 20 another level from map molecule number 93 11 17 21 residue density fit scale factor esses 93 11 17 22 density at point 0 0 cece eee eee 93 11 18 Parameters from map 93 11 18 1 mtz hklin for map 2 0 cee eee ee eens 93 11 18 2 mtz fp for map 06 eee I 93 11 18 38 mtz phi for map eee eee eens 93 11 18 4 mtz weighbt Jor map 00 ccc cece eee eee ees 94 11 18 5 mtz use weight for map sess 94 11 19 CPD BePunctions s 0 2 bnctee ee A eee Ae 94 11 19 1 wrte pdb nle nar a es e e a ene eee 94 11 19 2 wrte zeaidue range Ao pdb Dle 94 11 19 3 guick SaV AER REENEN e IRR Ed 94 11 20 Refmac FUNCtONS nseni n a e dais 95 11 20 1 set refmac counter sess ene 95 11 20 2 refrmac name 6 ccc eee e e een 95 11 20 38 owap map coloure ne 95 11 20 4 set keep map colour after refmac 0 2 0000 95 11 20 5 keep map colour after refmac State ooooooocoommm 95 11 21 Symmetry Hunctons ca 96 11 21 1 Set symmetry SlZE sopera doe de Vea See Des 96 11 21 2 get show symmetry sssesse eh 96 11 21 3 set show symmetry master sess 96 11 21 4
177. first dots object for imol with given name 11 63 6 n dots sets n dots sets imol Where mol is an integer number return the number of dots sets for molecule number imol 11 64 Pep flip Interface 11 64 1 pepflip pepflip imol chain id resno inscode altconf Where e imol is an integer number e chain id is a string e resno is an integer number e inscode is a string e altconf is a string pepflip the given residue 11 65 Rigid Body Refinement Interface 11 65 1 rigid body refine zone rigid body refine zone reso start resno_end chain id imol Where e reso_start is an integer number e resno_end is an integer number e chain id is a string 143 function function function function function Chapter 11 Scripting Functions 144 e mol is an integer number setup rigid body refine zone where we set the atom selection holders according to the arguments and then call execute_rigid_body_refine 11 65 2 set rigid body fit acceptable fit fraction set rigid body fit acceptable fit fraction f function Where f is a number set rigid body fraction of atoms in positive density 11 66 Add Terminal Residue Functions 11 66 1 set add terminal residue immediate addition set add terminal residue immediate addition i function Where 1 is an integer number set immediate addition of terminal residue call with i 1 for immediate addtion 11 66 2 add terminal residue add terminal residue imol chain id r
178. g 0 0 00 cee eee ee eee 138 11 62 2 set bond thickness 0 0 0 cece eee eens 138 11 62 3 set bond thickness intermediate atoms 138 11 62 4 set default representation type eee eee eee 138 11 62 5 get default bond thickness 000 eee eee eee 138 11 62 6 set draw zero occ markers 0 eee eee ee eee 139 XV xvi 11 62 7 set draw hydrogens ococoocccconnccccnnncccr 139 11 62 8 draw hydrogens state 0 cece eee eens 139 11 62 9 erapbics to Ca representation 00 cee eee eee 139 11 62 10 graphics to ca plus ligands representation 139 11 62 11 graphics to bonds no waters representation 139 11 62 12 graphics to bonds representation oooooocooocco o 139 11 62 13 graphics to ca plus ligands sec struct representation 140 11 62 14 graphics to sec struct bonds representation 140 11 62 15 graphics to rainbow representation 140 11 62 16 graphics to b factor representation sssssss 140 11 62 17 graphics to b factor cas representation 140 11 62 18 graphics to occupancy representation ss 140 11 62 19 graphics molecule bond type sssssususrsrsrrsese 140 11 62 20 set b factor bonds scale factor 0 0 2 eee eee 140 11 62 21 change model molecule representation mode 141 11 62 22 make baltand a ck uenee 141 11 62 23 clear ball and stick s
179. g Where e dots file is a string e imolis an integer number e show clash gui flag is an integer number pass a filename that contains molprobity s probe output in unformatted format Chapter 11 Scripting Functions 172 11 93 3 set do probe dots on rotamers and chis set do probe dots on rotamers and chis state function Where state is an integer number shall we run molprobity for on edit chi angles intermediate atoms 11 93 4 do probe dots on rotamers and chis state do probe dots on rotamers and chis state function return the state of if run molprobity for on edit chi angles intermediate atoms 11 93 5 set do probe dots post refine set do probe dots post refine state function Where state is an integer number shall we run molprobity after a refinement has happened 11 93 6 do probe dots post refine state do probe dots post refine state function show the state of shall we run molprobity after a refinement has happened 11 93 7 unmangle hydrogen name unmangle hydrogen name pdb_hydrogen_name function Where pdb hydrogen name is a string make an attempt to convert pdb hydrogen name to the name used in Coot and the refmac dictionary perhaps 11 93 8 set interactive probe dots molprobity radius set interactive probe dots molprobity radius r function Where r is a number set the radius over which we can run interactive probe bigger is better but slower default is 6 0 11 93 9 interactive probe dots mol
180. ge for the PTY phosphorylate active residue procedure A bit of fun overlay my ligands imol mov chain id mov resno mov imol ref procedure chain id ref resno ref A function for Overlaying ligands The transformation is applied to all the atoms of the molecule that contains the moving ligand label all CAs imol procedure label all atoms in residue imol chain id resno inscode procedure label all active residue atoms procedure sanitise alt confs atom info atom ls procedure Resets alt confs and occupancies of atoms in residue that have orphan alt loc at tributes sanitise alt confs in residue imol chain id resno inscode procedure sanitise alt confs active residue procedure Resets alt confs and occupancies of atoms in residue that have orphan alt loc at tributes Use the active residue print molecule names procedure save dialog positions to init file procedure multi chicken imol n colours procedure multiple maps of varying colour from a given map BALL_AND_STICK procedure simple enumeration Chapter 13 Scheme Scripting Functions 210 hilight binding site imol centre residue spec hilight colour radius procedure hilight colour is specified in degrees round the colour wheel starting at yellow e g 230 is purple pukka puckers imol procedure To paraphrase The distance of the plane of the base to the following phosphate is highly correlated to the pucker of the ribose An analysis of the structu
181. ge imol chain id start res no procedure stop res no sequence mutate and auto fit a residue range This presumes a protein sequence not nucleic acid The sequence is a string of one letter codes mutate and auto fit residue number chain id mol mol for map procedure residue type mutate and autofit whole chain This presumes a protein sequence not nucleic acid maf procedure a short hand for mutate and auto fit 3 letter code gt single letter residue type procedure return a char return A for unknown residue type mutate residue redundant procedure a wrapper for mutate single residue by seqno which uses slightly inconvenient single letter code Here residue type is the 3 letter code delete sidechain range procedure Delete back to the CB stub the side change in the range resno start to resno end 13 43 coot lsq lsq match type symbol gt number match type in procedure Internal type conversion for LSQ fitting Return a number according to the symbol match type in set match element procedure Create matchers 7 elements list ref start resno ref end resno ref chain id imol ref mov start resno mov end resno mov chain id imol mov match type Chapter 13 Scheme Scripting Functions 214 lsq match imol ref imol moving match list procedure The scripting interface to LSQ matching Pass molecule numbers for the reference imol ref and moving imol moving molecules and a match list The match list format is de
182. go to atom window sss eee eee eee 113 11 37 2 set go to atom chain residue atom name 113 11 37 3 update go to atom from current position 113 11 37 4 atom spec to atom index ssseseeeeeeeeeeees 113 11 37 5 full atom spec to atom index sseesesssses 114 11 37 6 update go to atom window on changed mol 114 11 37 7 update go to atom window on new mol 114 11 37 8 oet go to atom molecule 00 cece eee 114 11 38 Map and Molecule Control 114 11 38 1 pGost displase comtrot windomw cece e ee 114 11 38 2 set map displayed 0 0 cece eee ee eee 115 11 38 3 set mol displayed 0 0 e cece eee eee eee 115 11 38 4 zet molactve cece es 115 11 38 5 molis dieplaved 0 00 cece eee een eee eee 115 11 38 6 mol is active 1 ccc nett nees 115 11 38 7 map is displayed 0 0 cece eee eee eee 115 11 38 8 set all maps displayed 0 0 00 e cece eee eee 116 11 38 9 set all models displayed and active 004 116 11 38 10 sbow epacegroup cece eee n 116 11 39 Align and Mutate 000 cece cee eee ees 116 xii 11 39 1 align and mutate 0 0 cece eee eh 116 11 39 2 set alignment gap and space penalty 116 11 39 3 align to closest chain 0 0 cece eee eee eee eee 117 11 40 Renumber Residue Range 117 11 40 1 renumber residue range sss 117 11 40 2 change residue number 000 cece eee
183. h Ae 64 11 1 2 vt surface status 0 0 00 eee n 64 11 2 Startup Functions enis e nne 64 11 2 zet preler methon eee nee eee 64 11 2 2 prefer Python vas ete ikke a ates 64 11 3 File System Functions 0 c cece cee eee eee eens 64 11 3 1 make directory maybe sess 64 11 3 2 set show paths in display manager ssssss 65 11 3 8 show paths in display manager state sess 65 11 3 4 add coordinates glob extension 000 e eee eee 65 11 3 5 add data glob etensgton 0 e eee eee eee ees 65 11 3 6 add dictionary glob extension 0 0c eee eee 65 11 3 7 add map glob extension 00sec eee eee eee eee 65 11 3 8 remove Coordinates glob etensgion eee ee ee 65 11 3 9 remoee data glob evtenzgon 0 000 e cece eee ees 65 11 3 10 remove dictionary glob extension 0 20 ee 66 11 3 11 remove map glob extensgion 02 e cece eee eee 66 11 3 12 set sticky sort by date 0 0 cece eee eee ee 66 11 3 13 unset sticky sort by date 00 cece eee eee ee 66 11 3 14 oet Dlter Dleselechon Dlenamen 000s eee 66 11 3 15 filter fileselection filenames state 00 c eee eee 66 11 8 16 file type coords ssssssssesees anerer 66 11 8 17 open coords dialog 0 6 cece eee eee eee 66 Dat Widget Utilities ce resti E Ale 67 TPAD untfo dialog ui e riel eia 67 11 4 2 info dialog and text 0 0 0 ccc eee e ees 67 11 5 MTZ and data handling utilities 0
184. h bonds s ate function Where state is an integer number show H bond environment distances If state is 0 bump distances are turned off otherwise H bond distances are turned on 11 47 4 show environment distances state show environment distances state function show the state of display of the environment distances 11 47 5 set environment distances distance limits set environment distances distance limits min dist max dist function Where Chapter 11 Scripting Functions 127 e min_dist is a number e maz dist is a number min and max distances for the environment distances 11 48 Pointer Functions 11 48 1 set show pointer distances set show pointer distances istate function Where istate is an integer number turn on or off the pointer distance by passing 1 or 0 11 48 2 show pointer distances state show pointer distances state function show the state of display of the pointer distances 11 49 Zoom Functions 11 49 1 scale zoom scale zoom f function Where f is a number scale the view by f external scripting interface with redraw 11 49 2 zoom factor zoom factor function return the current zoom factor 11 49 3 set smooth scroll do zoom set smooth scroll do zoom i function Where i is an integer number set smooth scroll with zoom 11 49 4 smooth scroll do zoom smooth scroll do zoom function return the state of the above system 11 50 CNS Data Functions Chapter 11 Scripting Fu
185. hases sees 197 M BEER Ee e e ey 118 run state file p daa 101 run state file maybe oooooocooooo 101 S sanitise alt confs o o ooooooooommmm o 209 sanitise alt confs active residue 209 sanitise alt confs in residue 209 save annotations esee eene 210 save coordinates cece eee eee 110 save dialog positions to init file 209 save previous map colour s 85 Save state coup o P enU irr 101 save state file e lebe RET 101 save symmetry coords sese 97 Save vieWS c PUDE I ai 133 scaleccell eri pideei td ete oes EL 173 SCALE ZOOM LA 127 Scheme representation suse 206 Score residue range fit to map 125 SCreendump jimage 6 cece cece 76 scroll by wheel mouse state 77 scroll wWheel map nbesss EN e 84 secondary structure restraints type 123 seqnum from serial number 68 set accept reject dialog position 106 Set active map drag flag 85 set add terminal residue default residue PP ie ets zs BAI es 145 set add terminal residue do post refine FASE era eM Ret IN nce ROV wen IND 145 224 set add terminal residue immediate addition IA Al ia 144 set alignment gap and space penalty 116 set all maps displayed asnasnnnnn 116 set all models displayed and active 116 set atom attribute o o o ooooomommmmmo 108 set atom stri
186. hat happens when the download button is pressed This is run in a thread so it can t do any graphics stuff return t if tar file was successfully downloaded and untared and f if not get revision from string s r procedure used in downloading new version coot split version string s r procedure e g input coot 0 6 2 pre 1 revision 27651n output coot 0 6 2 pre 1 revision 2765 load default sequence procedure In the first case the sequence is assigned to the closest match model sequence to target sequence subsequently only chains without a sequence associated with them are candidates for matching The protein sequence has to have at least 95 sequence identity with the target sequence in default seq Chapter 13 Scheme Scripting Functions coot updates error handler key args not really for public manipulation update self keep a copy of the old directories around in a directory named after expir chiral centre inverter This should almost all be c code so that Bernie doesn t have to redo temporary then get drug via wikipedia drug name 211 procedure procedure ation time procedure it This is procedure return a string DB00xxxx mol or some such this is the file name of the mdl mol file from drugbank Or f undefined on fail Test result with string chiral center inverter Americans coot has pygtk to determine if we have pygtk 13 38 snarf coot docs glob pat dir ret
187. here is no mtz file associated with that map it was generated from a CCP4 map file say 11 18 3 mtz phi for map mtz phi for map mol man function Where imol_map is an integer number return the phases column in mtz file that was use to generate the map return 0 when there is no mtz file associated with that map it was generated from a CCP4 map file say Chapter 11 Scripting Functions 11 18 4 mtz weight for map mtz weight for map imol map function Where mol map is an integer number return the weight column in the mtz file that was use to generate the map return 0 when there is no mtz file associated with that map it was generated from a CCP4 map file say or no weights were used 11 18 5 mtz use weight for map mtz use weight for map imol map function Where mol map is an integer number return flag for whether weights were used that was use to generate the map return 0 when no weights were used or there is no mtz file associated with that map 11 19 PDB Functions 11 19 1 write pdb file write pdb file imol file name function Where e imolis an integer number e file name is a string write molecule number mol as a PDB to file file name 11 19 2 write residue range to pdb file write residue range to pdb file imol chainid resno_start resno_end function filename Where e imolis an integer number e chainid is a string e resno_start is an integer number e resno_end is an integer number e filename is a string
188. here is no such object with name obj name then create a new one Maybe you want the generic object to be cleaned if it exists before returning this function does not do that generic objects gui procedure display a GUI for generic objects reduce on pdb file imol pdb in pdb out procedure return status probe procedure run molprobity well reduce and probe to make generic objects and display the generic objects gui write reduce het dict imol reduce het dict file name procedure Write the connectivity for the non standard non water residues in the given molecule for which we have the dictionary Don t return anything interesting interactive probe is 0K x procedure gets set the first time we run interactive probe Takes values unset initial value yes and no interactive probe procedure run probe interactively which in the current implementation means that this func tion can run during a edit chi angles manipulation or after a real space refine zone Thus function presumes that there are 2 pdb files in the current directory one of which is the reference pdb file and the other is a pdb file containing the tmp moving atom set The function takes arguments for the centre of the probe dots and the radius of the probe dots sphere The chain id and residue number are also needed to pass as arguments to probe probe local sphere imol radius procedure Update the generic objects probe dots from residues within
189. hi angles gui for the given residue return a status of 0 if it failed to fined the residue return a value of 1 if it worked 11 75 3 setup torsion general setup torsion general state function Where state is an integer number beloved torsion general at last makes an entrance onto the Coot scene 11 76 Masks 11 76 1 mask map by molecule mask map by molecule map_mol_no coord_mol_no invert_flag function Where e map_mol_no is an integer number e coord mol_no is an integer number e invert_flag is an integer number generate a new map that has been masked by some coordinates mask map by molecule map no mol no invert creates and displays a masked map cuts down density where the coordinates are invert is 0 If invert is 1 cut the density down where there are no atoms atoms 11 76 2 set map mask atom radius set map mask atom radius rad function Where rad is a number set the atom radius for map masking Chapter 11 Scripting Functions 11 76 3 map mask atom radius map mask atom radius get the atom radius for map masking 11 77 check Waters Interface 11 77 1 delete checked waters baddies delete checked waters baddies imol b_factor_lim map sigma lim min_dist max_dist part_occ_contact_flag zero_occ_flag logical_ operator_and_or_flag Where e mol is an integer number e b_factor_lim is a number e map sigma lim is a number e min dist is a number e moar dist is a number e part occ contact flag is an
190. i is O to never run this state file at startup iis 1 to get a dialog option this is the default and i is 2 to run the commands without question 3 10 4 Key Binding Power users of Coot might like to write their own functions and bind that function to a keyboard key How do they do that By using the add key binding function add key binding function name key function where key is a quoted string note that upper case and lower case keys are distinguished activate get upper case key binding you need to chord the shift key for example add key binding Refine Active Residue with Auto accept x refine active residue Have a look at the key bindings section on the Coot wiki for several more examples 3 10 5 User Defined Functions Power users of Coot might also like to write their own functions that occur after picking an atom or a number of atoms user defined click n clicks udfunc define a function func which runs after the user has made n clicked atom picks func is called with a list of atom specifiers the first member of which is the molecule number 3 11 Backups and Undo By default each time a modification is made to a model the old coordinates are written out The backups are kept in a backup directory and are tagged with the date and the history number lower numbers are more ancient The Undo function discards the current molecule and loads itself from the most recent backup coordin
191. ications that need to be made to match the model sequence to the assigned sequence s Call this when the associated sequence s have been read in already residue range gui procedure Notice that we are not dealing with insertion codes user mods gui imol pdb file name procedure USER MODS gui rename residue gui procedure simple rename residue GUI water coordination gui procedure close button min max residues from atom specs specs procedure return a list or f e g if not in same chain and molecule 13 12 ncs Skip to next ncs chain direction procedure Skip the residue in the next chain typically of a molecule with NCS with the same residue number If on the last chain then wrap to beginning If it can t find anything then don t move and put a message in the status bar single manual ncs ghost imol resno start resno end ref chain procedure peer chain We can only see one peer at a time with this each time we do a clear ncs ghost matrices manual ncs ghosts imol resno start resno end chain id list procedure chain id list is list A B C D e the reference target master chain id first and then the peers This allows us to add many peers at the same time unlike above function ncs master chain id imol procedure Return the first master chain id usually there is only one of course or f ncs ligand imol protein ncs master chain id imol ligand chain id ligand procedure resno ligand start resn
192. ick selection procedure used in Extensions gt Representation Ball amp Stick rigid body refine by residue ranges procedure rigid body refine using residue ranges Takes 2 arguments the first is the molecule number the second is a list of residue ranges A residue range is list chain id resno start resno end find aligned residue type procedure add terminal residue is the normal thing we do with an aligned sequence but also we can try ton find the residue type of a residue in the middle of the chain that is modelled as an ALA say molecule has hydrogens imol procedure schemify function post manipulation hook procedure pre release procedure Return a boolean molecule number list procedure Return a list of molecule numbers closed and open The elements of the returned list need to be tested against is valid model molecule first n n Is procedure first n fields of ls if length Is is less than n return ls if ls is not a list return ls If n is negative return ls directory is modifiable prefix dir procedure Test for prefix dir 1 being a string 2 existing 3 being a directory 4 modifiable by user ie u rwx prefix dir must be a string Return t or f absolutify file name procedure return an absolute file name for file name or f file name directory file name procedure return the directory component of file name leave on if it s there Note x no nn most recen
193. idget Functions 11 37 1 post go to atom window post go to atom window function Post the Go To Atom Window 11 37 2 set go to atom chain residue atom name set go to atom chain residue atom name t1_chain_id iresno function t3 atom name Where e l chain id is a string e iresno is an integer number e LN alom name is a string set the go to atom specification It seems important for swig that the char arguments are const char gchar or else we get wrong type of argument error on say A not const Returns the success status of the go to 0 for fail 1 for success 11 37 3 update go to atom from current position update go to atom from current position function update the Go To Atom widget entries to atom closest to screen centre 11 37 4 atom spec to atom index atom spec to atom index mol chain resno atom name function Where e mol is an integer number e chain is a string e resno is an integer number e atom name is a string what is the atom index of the given atom Chapter 11 Scripting Functions 114 11 37 5 full atom spec to atom index full atom spec to atom index imol chain resno inscode atom_name function altloc Where e mol is an integer number e chain is a string e resno is an integer number e inscode is a string e atom name is a string e altloc is a string what is the atom index of the given atom 11 37 6 update go to atom window on changed mol update go to at
194. ie list return value chain id res no ins code all residues imol procedure Return residue specs for all residues in imol each spec is preceeded by t residues with alt confs imol procedure Return a list of all residues that have alt confs where a residue is specified thusly list chain id resno ins code residue alt confs imol chain id res no ins code procedure Return a list of all the altconfs in the residue Typically this will return list or list A B res spec gt chain id res spec procedure simple extraction function res spec gt res no res spec procedure simple extraction function Chapter 13 Scheme Scripting Functions 209 res spec gt ins code res spec procedure simple extraction function residue spec gt atom for centre imol chain id res no ins code procedure Return f if no atom can be found given the spec else return a list consisting of the atom name and alt conf specifier Choose an atom that is called CA Failing that choose the first atom update go to atom from current atom procedure flip active ligand procedure delete atom by active residue procedure Typically one might want to use this on a water but it deletes the nearest CA currently Needs a re think Should active atom just return the nearest atom and not be clever about returning a CA merge solvent chains imol procedure mutate by overlap imol chain id in resno tlc procedure change chain ids with residue ran
195. imol ref procedure target is my molecule ref is the homologous high res model 13 6 cns2coot cns coot 2fofc coeffs fofc coeffs model pdb procedure Read in cns coeff data given filenames and a pdb molecule filename to make maps 13 7 group settings rapper dir procedure The rapper installation dir This is just a guess that it is installed in the users home directory 13 8 clear backup delete coot backup files action type procedure clear backup gui procedure Return t or f depending on if the GUI dialog was shown it isn t show if there are no files to delete clear backups maybe procedure Return a status f or t did the GUI run Note that clear backup gui returns either t or f too If this function returns f then coot real exit just exits with coot real exit Oth erwise we wait for the GUI Chapter 13 Scheme Scripting Functions 187 13 9 quat convert matrix gt quaternion procedure convert a view matrix to a view quaternion to set Coot view internals set view matrix m00 m10 m20 m01 m11 m21 m02 m12 m22 procedure Set the view matrix 13 10 filter filter fn ls procedure Basic scheme function filter the objects in list ls by function fn e g filter even list 0 1 2 3 gt 0 2 13 11 coot gui run gtk pending events procedure coot gui procedure Fire up the coot scripting gui This function is called from the main C code of coot Not much use if you don t hav
196. ing way 13 41 coot crash catcher filter fn ls procedure Basic scheme function filter the objects in list ls by function fn e g filter even list 0 1 2 3 gt 0 2 string concatenate ls procedure simple scheme functions to concat the strings in ls ls must contain only strings directory files dir procedure The following functions from PLEAC guile version thereof of course or define a utility function for this glob pat dir procedure return a list of file names that match pattern pat in directory dir run command strings cmd args data list procedure Return the strings screen output of cmd reversed or f if command was not found command in path cmd procedure Return t or f make gdb script procedure get gdb strings procedure return f or list of strings make gui procedure gui Chapter 13 Scheme Scripting Functions 213 13 42 mutate in scheme mutate chain imol chain id sequence procedure Mutate chain id of molecule number imol given sequence This presumes a protein sequence The number of residues in chain id must match the length of sequence multi mutate procedure An internal function of mutate This presumes a protein sequence mutate residue range imol chain id start res no stop res no sequence procedure The stop res no is inclusive so usage e g mutate residue range 0 A 1 2 AC This presumes a protein sequence not nucleic acid mutate and autofit residue ran
197. ings Coordinate IDs are explained in detail in the mmdb manual Briefly the string should be formed in this manner mdl chn seq res ic atm elm aloc e g 1 A 12 130 CA Be g this molecule was a map or a closed molecule 14 the same one as in the CCP4 program SUPERPOSE Chapter 4 Coordinate Related Features 25 4 21 Least Squares Fitting There is a simple GUI for this Calculate gt LSQ Superpose The scripting interface to LSQ fitting is as follows simple 1sq match ref start resno ref end resno ref chain id imol ref mov start resno mov end resno mov chain id imol mov match type where e ref start resno is the starting residue number of the reference molecule e ref end resno is the last residue number of the reference molecule e mov start resno is the starting residue number of the moving molecule e mov end resno is the last residue number of the moving molecule e match type is one of CA main or all e g simple 1sq match 940 950 A O 940 950 A 1 main More sophisticated match molecule number 1 chain B on to molecule number 0 chain A define match list 840 850 A 440 450 B a11 define match list 940 950 A 540 550 B main clear lsq matches set match element match1 set match element match2 1sq match 0 1 match molecule number 1 onto molecule number 0 4 22 Ligand Overlaying The scripting function overlap ligands imol ligand imol ref chain id ref resno ref
198. integer number e zero occ flag is an integer number e logical_operator_and_or_flag is an integer number Delete waters that are fail to meet the given criteria 11 78 Trim 11 78 1 trim molecule by map trim molecule by map imol_coords imol_map map level delete_or_zero_occ_flag Where e imol coords is an integer number e imol map is an integer number e map level is a number e delete or zero occ flag is an integer number 154 function function function cut off delete or give zero occupancy atoms in the given molecule if they are below the given map absolute level 11 79 External Ray Tracing 11 79 1 raster3d raster3d rd3 filename Where d filename is a string create a r3d file for the current view function Chapter 11 Scripting Functions 11 79 2 set raster3d bond thickness set raster3d bond thickness f Where f is a number set the bond thickness for the Raster3D representation 11 79 3 set raster3d atom radius set raster3d atom radius f Where f is a number set the atom radius for the Raster3D representation 11 79 4 set raster3d density thickness set raster3d density thickness f Where f is a number set the density line thickness for the Raster3D representation 11 79 5 set renderer show atoms set renderer show atoms istate Where istate is an integer number set the flag to show atoms for the Raster3D representation 11 79 6 set raster3d bone thickness set raster3d bone thic
199. inter label set model fit refine place atom at pointer label txt function Where tzt is a string Allow the changing of Model Fit Refine button label from Place Atom at Pointer 11 12 5 post other modelling tools dialog post other modelling tools dialog function display the Other Modelling Tools dialog 11 12 6 set refinement move atoms with zero occupancy set refinement move atoms with zero occupancy state function Where state is an integer number shall atoms with zero occupancy be moved when refining default 1 yes 11 12 7 refinement move atoms with zero occupancy state refinement move atoms with zero occupancy state function return the state of shall atoms with zero occupancy be moved when refining 11 13 Backup Functions 11 13 1 make backup make backup imol function Where mol is an integer number make backup for molecule number imol Chapter 11 Scripting Functions 11 13 2 turn off backup turn off backup imol function Where mol is an integer number turn off backups for molecule number imol 11 13 3 turn on backup turn on backup imol function Where mol is an integer number turn on backups for molecule number imol 11 13 4 backup state backup state imol function Where mol is an integer number return the backup state for molecule number imol return 0 for backups off 1 for backups on 1 for unknown 11 13 5 set have unsaved changes set have unsaved changes imol function Wh
200. ion Where f is a number set the size of the displayed symmetry 11 21 2 get show symmetry get show symmetry function is symmetry master display control on 11 21 3 set show symmetry master set show symmetry master state function Where state is an integer number set display symmetry master controller 11 21 4 set show symmetry molecule set show symmetry molecule mol_no state function Where e mol_no is an integer number e state is an integer number set display symmetry for molecule number mol_no pass with state 0 for off state 1 for on 11 21 5 symmetry as calphas symmetry as calphas mol_no state function Where e mol_no is an integer number e state is an integer number display symmetry as CAs pass with state 0 for off state 1 for on 11 21 6 get symmetry as calphas state get symmetry as calphas state imol function Where mol is an integer number what is state of display CAs for molecule number mol no return state 0 for off state 1 for on Chapter 11 Scripting Functions 11 21 7 set symmetry molecule rotate colour map set symmetry molecule rotate colour map imol state function Where e imol is an integer number e state is an integer number set the colour map rotation i e the hue for the symmetry atoms of molecule number imol 11 21 8 symmetry molecule rotate colour map state symmetry molecule rotate colour map state imol function Where mol is an integer number should there be
201. ion of the Rotate Translate Residue Range dialog 11 27 16 set accept reject dialog position set accept reject dialog position x pos y_pos Where e r pos is an integer number e y_pos is an integer number set position of the Accept Reject dialog 11 27 17 set ramachandran plot dialog position set ramachandran plot dialog position x_pos y pos Where e r pos is an integer number e y_pos is an integer number set position of the Ramachadran Plot dialog 11 27 18 set edit chi angles dialog position set edit chi angles dialog position x pos y pos Where e r pos is an integer number e y_pos is an integer number set edit chi angles dialog position 11 27 19 set rotamer selection dialog position set rotamer selection dialog position x_pos y pos Where e r pos is an integer number e y_pos is an integer number set rotamer selection dialog position 106 function function function function function Chapter 11 Scripting Functions 11 28 Smooth Scrolling 11 28 1 set smooth scroll flag set smooth scroll flag v Where v is an integer number set smooth scrolling 11 28 2 get smooth scroll get smooth scroll return the smooth scrolling state 11 28 3 set smooth scroll steps set smooth scroll steps i Where 1 is an integer number set the number of steps in the smooth scroll Set more steps e g 50 for more smoothness default 10 11 28 4 set smooth scroll limit set smooth scroll lim
202. ipting Functions 147 e resno is an integer number e ins code is a string e do delete dialog is an integer number delete all atoms in residue that are not main chain or CB 11 67 7 delete hydrogens delete hydrogens imol function Where mol is an integer number delete all hydrogens in molecule Returns number of hydrogens deleted 11 68 Mainchain Building Functions 11 68 1 db mainchain db mainchain imol chain id iresno_start iresno_end direction_string function Where e imolis an integer number e chain id is a string e iresno_start is an integer number e iresno end is an integer number e direction string is a string CA mainchain conversion 11 69 Rotatmer Functions 11 69 1 set rotamer search mode set rotamer search mode mode function Where mode is an integer number set the mode of rotamer search options are ROTAMERSEARCHAUTOMATIC ROTAMERSEARCHLOWRES aka backrub rotamers ROTAMERSEARCH HIGHRES with rigid body fitting 11 69 2 set rotamer lowest probability set rotamer lowest probability f function Where f is a number For Dunbrack rotamers set the lowest probability to be considered Set as a percent age i e 1 00 is quite low For Richardson Rotamers this has no effect 11 69 3 set rotamer check clashes set rotamer check clashes i function Where 1 is an integer number set a flag 0 is off 1 is on Chapter 11 Scripting Functions 148 11 69 4 auto fit best rotamer
203. ir force n cycles make molecules flag ccp4i project dir f col sig f col r free col extra params include weight params list procedure Return t if the list of strings params list contains a string beginning with WEIGHT If not return f Chapter 13 Scheme Scripting Functions 197 get refmac extra params procedure If refmac extra params is defined as a list of strings then return that else read the file refmac extra params Return a list a list of strings run refmac for phases procedure this is not run as a sub thread no useful return value 13 25 a rapper gui rapper dir procedure something that the user sets a rapper gui loop building tool procedure loop building tool is either rapper or ARP wARP 13 26 extra top level my button callback procedure This is what to do when the button is pressed It can be any guile or coot function my top level procedure define a simple window and put a button in it 13 27 raster3d from scheme render image procedure run raster3d raytrace procedure Run either raster3d or povray 13 28 check for updates get stable release from server string str procedure Is this true get stable release from coot version procedure Needs testing notify of new version str procedure show the dialog download binary dialog procedure version string is something like coot 0 6 pre 1 revision 2060 directory is modifiable prefix dir procedure Test for p
204. is a string e seq is a string 165 function function Assign a PIR sequence to a given chain in the molecule If the chain of the molecule already had a chain assigned to it then this will overwrite that old assignment with the new one 11 86 4 assign sequence from file assign sequence from file imol file Where e mol is an integer number e file is a string Assign a sequence to a given molecule from whatever sequence file 11 86 5 assign sequence from string assign sequence from string imol chain_id_in seq Where e mol is an integer number e chain id mn is a string e seq is a string Assign a sequence to a given molecule from a simple string 11 86 6 delete all sequences from molecule delete all sequences from molecule imol Where imol is an integer number Delete all the sequences from a given molecule function function function Chapter 11 Scripting Functions 166 11 86 7 delete sequence by chain id delete sequence by chain id imol chain_id_in function Where e mol is an integer number e chain_id_in is a string Delete the sequence for a given chain_id from a given molecule 11 87 Surface Interface 11 87 1 do surface do surface imol istate function Where e imol is an integer number e state is an integer number draw surface of molecule number imol if state 1 draw the surface normal representation goes away if state 0 don t draw surface 11
205. is an integer number reset temperature factor for all moved atoms to the default for new atoms usually 30 11 31 5 get reset b factor moved atoms state get reset b factor moved atoms state function return the state if temperature factors shoudl be reset for moved atoms 11 31 6 set atom attribute set atom attribute imol chain_id resno Ins code atom name alt_conf function attribute_name val Where e imol is an integer number e chain id is a string e resno is an integer number e ins code is a string e atom name is a string Chapter 11 Scripting Functions 109 e alt_conf is a string e attribute name is a string e val is a number set a numberical attibute to the atom with the given specifier Attributes can be x y z B occ and the attribute val is a floating point number 11 31 7 set atom string attribute set atom string attribute imol chain_id resno ins_code atom name function alt_conf attribute name attribute value Where e imolis an integer number e chain id is a string e resno is an integer number e ins code is a string e atom name is a string e alt_conf is a string e attribute name is a string e attribute value is a string set a string attibute to the atom with the given specifier Attributes can be atom name alt conf element or segid 11 31 8 set residue name set residue name imol chain id res no ins_code new residue name function Where e imolis an integer numb
206. is an integer number set the flag to do flat shading rather than smooth shading for solid density surface Default is 1 on 11 9 Interface Preferences 11 9 1 set scroll by wheel mouse set scroll by wheel mouse istate function Where istate is an integer number Some people like Phil Evans don t want to scroll their map with the mouse wheel To turn off mouse wheel recontouring call this with istate value of 0 11 9 2 scroll by wheel mouse state scroll by wheel mouse state function return the internal state of the scroll wheel map contouring 11 9 3 set default initial contour level for map set default initial contour level for map n_sigma function Where n_sigma is a number set the default inital contour for 2FoFc style map in sigma 11 9 4 set default initial contour level for difference map set default initial contour level for difference map function n_sigma Where n_sigma is a number set the default inital contour for FoFc style map in sigma 11 9 5 print view matrix print view matrix function print the view matrix to the console useful for molscript perhaps Chapter 11 Scripting Functions 11 9 6 get view quaternion internal get view quaternion internal element function Where element is an integer number internal function to get an element of the view quaternion The whole quaternion is returned by the scheme function view quaternion 11 9 7 set view quaternion set view quaternion ijkl func
207. it default 0 0 11 16 12 set residue density fit scale factor set residue density fit scale factor f function Where f is number set the scale factor for the Residue Density fit analysis Chapter 11 Scripting Functions 11 17 Density Functions 11 17 1 set map line width set map line width w Where w is an integer number draw the lines of the chickenwire density in width w 11 17 2 map line width state map line width state return the width in which density contours are drawn 11 17 3 make and draw map make and draw map mtz_file_name f col phi_col weight use weights is diff map Where e mtz_file name is a string e f_col is a string e phi_col is a string e weight is a string e use weights is an integer number e is diff map is an integer number make a map from an mtz file simple interface function function function given mtz file mtz_file name and F column f_col and phases column phi_col and op tional weight column weight_col pass use_weights 0 if weights are not to be used Also mark the map as a difference map is diff map 1 or not is diff map 0 be cause they are handled differently inside coot Returns 1 on error else return the new molecule number 11 17 4 make and draw map with refmac params make and draw map with refmac params mtz_file_name a b weight function use weights is_diff_ map have_refmac_params fobs_col sigfobs_col r_free_col sensible f free_col
208. it lim Where lim is a number do not scroll for distances greater this limit 11 29 Font Size 11 29 1 set font size set font size i Where 1 is an integer number set the font size 11 29 2 get font size get font size return the font size Returns 1 small 2 medium default 3 large 11 29 3 set font colour set font colour red green blue Where e red is a number e green is a number e blue is a number set the colour of the atom label font the arguments are in the range 0 51 107 function function function function function function function Chapter 11 Scripting Functions 108 11 30 Rotation Centre 11 30 1 go to ligand go to ligand function centre on the ligand of the active molecule if we are already there centre on the next hetgroup etc 11 31 Atom Selection Utilities 11 31 1 clear pending picks clear pending picks function clear pending picks stop coot thinking that the user is about to pick an atom 11 31 2 set default temperature factor for new atoms set default temperature factor for new atoms new_b function Where new_b is a number set the default temperature factor for newly created atoms initial default 20 11 31 3 default new atoms b factor default new atoms b factor function return the default temperature factor for newly created atoms 11 31 4 set reset b factor moved atoms set reset b factor moved atoms state function Where state
209. ivate function is a thunk missing atoms gui imol procedure Make an interesting things GUI for residues with missing atoms generic buttons dialog dialog name button list procedure button list is a list of pairs improper list the first item of which is the button label text the second item is a lambda function what to do when the button is pressed Chapter 13 Scheme Scripting Functions 190 generic interesting things imol gui title string residue test func procedure Generic interesting things gui user passes a function that takes 4 args the chain id resno inscode and residue serial number should it be needed and returns either iif or something interesting e g a label value It is the residue test func of the residue matching criteria function generic number chooser number list default option value hint text procedure go button label go function A gui that makes a generic number chooser the go function is a lambda function that takes the value of the active menu item as a number generic molecule chooser hbox hint text procedure pack a hint text and a molecule chooser option menu into the given vbox return the option menu and model molecule list file selector entry hbox hint text procedure Return an entry the widget is inserted into the hbox passed to this function cootaneer gui imol procedure Cootaneer gui view saver gui procedure The gui for saving views add view to views panel view name view number
210. kness f Where f is a number set the bone skeleton thickness for the Raster3D representation 11 79 7 set raster3d shadows enabled set raster3d shadows enabled state Where state is an integer number turn off shadows for raster3d output give argument 0 to turn off 11 79 8 set raster3d water sphere set raster3d water sphere istate Where istate is an integer number set the flag to show waters as spheres for the Raster3D representation spheres 0 the usual stars 11 79 9 raster screen shot raster screen shot run raster3d and display the resulting image 155 function function function function function function function 1 show as function Chapter 11 Scripting Functions 156 11 80 Superposition SSM 11 80 1 superpose superpose imoll imol2 move_imol2_ flag function Where e moll is an integer number e imol2 is an integer number e move imol2 flag is an integer number simple interface to superposition Superpose all residues of imol2 onto imoll imoll is reference we can either move imol2 or copy it to generate a new molecule depending on the vaule of move imol2 flag 1 for move 0 for copy 11 80 2 superpose with chain selection superpose with chain selection imoll imol2 chain_imoll chain_imol2 function chain used flag imoll chain used flag imol2 move imol2 copy flag Where e imoll is an integer number e imol2 is an integer number e chain mol is
211. letter code Returns the new molecule number if not 1 error 11 42 3 run script run script filename function Where filename is a string run script file 11 43 Regularization and Refinement 11 43 1 add planar peptide restraints add planar peptide restraints function add a restraint on peptides to make them planar This adds a 5 atom restraint that includes both CA atoms of the peptide Use this rather than editting the mon lib list cif file Chapter 11 Scripting Functions 119 11 43 2 remove planar peptide restraints remove planar peptide restraints function remove restraints on peptides to make them planar 11 43 3 add omega torsion restriants add omega torsion restriants function add restraints on the omega angle of the peptides that is the torsion round the peptide bond Omega angles that are closer to 0 than to 180 will be refined as cis peptides and of course if omega is greater than 90 then the peptide will be refined as a trans peptide this is the normal case 11 43 4 remove omega torsion restriants remove omega torsion restriants function remove omega restraints on CIS and TRANS linked residues 11 43 5 set refinement immediate replacement set refinement immediate replacement istate function Where istate is an integer number set immediate replacement mode for refinement and regularization You need this call with istate 1 if you are scripting refinement regularization 11 43 6 refin
212. ligand_new imol_current chain id ligand current resno ligand current Where e imol_ligand_new is an integer number e chain id ligand new is a string e resno ligand mew is an integer number e imol current is an integer number e chain id ligand current is a string e resno ligand current is an integer number Copy a molecule with addition of a ligand and a deletion of current ligand This function is used when adding a new modified ligand to a structure It creates a new molecule that is a copy of the current molecule except that the new ligand is added and the current ligand residue is deleted 11 6 15 exchange chain ids for seg ids exchange chain ids for seg ids imol function Where mol is an integer number Experimental interface for Ribosome People Ribosome People have many chains in their pdb file they prefer segids to chainids chainids are only 1 character But coot uses the concept of chain ids and not seg ids mmdb allow us to use more than one char in the chainid so after we read in a pdb let s replace the chain ids with the segids Will that help 11 7 Library and Utility Functions 11 7 1 coot version coot version function the coot version string Returns something like coot 0 1 3 New versions of coot will always be lexograph ically greater than previous versions 11 7 2 svn revision svn revision function return the subversion revision number of this build Used in finding updates Ch
213. lip residue i1 9 4 23 i eu bey 192 get font Size viles iie alas Died 107 get gdb strings 0 eee eee eee 212 Set map Cadius eee eee eee 92 Set map sanpling rate 87 get mdl latest time sss 193 get molecule bonds colour map rotation 103 get monomer vis See dell nup XD e eue 118 get option menu active item 188 get option menu active molecule 188 get refmac extra params 197 get reset b factor moved atoms state 108 get revision from string 210 get sbase monomer 6 eee eee eee 176 get sbase monomer and overlay 193 get show symmetry eese 96 Set sbow opnit cell ss 102 get smooth scroll cece eee eee 107 get stable release from coot version 197 get stable release from server string 197 got symmetry oron ngese iba 179 get symmetry as calphas state 96 get url sir i loose o d 192 get view quaternion internal 78 get write conect record state 178 gln asn b factor outliers 129 f Ko So Seite hemes e WR 205 211 212 go to ligand cece eee 108 go to residue by spec cece eee 192 goosh command eee eens 203 211 Function Index goosh command with file input 203 graphics comma key pressed hook 208 graphics dot key pressed hook 208 graphics draw lesse 104
214. llback function is a function that takes a molecule number as an argument generic chooser and entry chooser label entry hint text procedure defaut entry text callback function A pair of widgets a molecule chooser and an entry The callback function is a function that takes a molecule number and a text string generic chooser entry and file selector chooser label procedure chooser filter entry hint text default entry text file selector hint callback function Create a window Return a pair of widgets a molecule chooser and an entry The callback function is a function that takes a molecule number and 2 text strings e g chain id and file name chooser filter is typically valid map molecule or valid model molecule generic chooser and file selector chooser label chooser filter procedure file selector hint default file name callback function Create a window Return a pair of widgets a molecule chooser and an entry callback function is a function that takes a molecule number and a file name chooser filter is typically valid map molecule or valid model molecule coot menubar menu menu label procedure If a menu with label menu label is not found in the coot main menubar then create it and return it If it does exist simply return it add simple coot menu menuitem menu menu item label procedure activate function Given that we have a menu e g one called Extensions provide a cleaner interface to adding something to it act
215. lue should be f if there was a problem or some value where we can check that pisa analyse ran probably a directory It is not clear right now where the output is going config files has PISA WORK ROOT coot pisa but things seems to be written to DATA BOOT home emsley ccp4 ccp4 6 1 3 share pisa which seems like a bug or something like it in pisa Needs rechecking cached pisa analysis dir procedure needs fleshing out see notes for prep for pisa parse pisa interfaces imol sxml entity procedure pdb_entry pdb code status n interfaces interface id type n occ int area int solv en pvalue stab en css overlap x rel fixed h bonds n_bonds bond chain 1 res 1 seqnum 1 inscode 1 atname 1 chain 2 res 2 seqnum 2 inscode 2 atname 2 dist salt bridges n bonds bond chain 1 res 1 seqnum 1 inscode 1 atname 1 chain 2 res 2 seqnum 2 inscode 2 atname 2 dist ss bonds n bonds bond chain 1 res 1 seqnum 1 inscode 1 atname 1 chain 2 res 2 seqnum 2 inscode 2 atname 2 dist cov bonds n bonds bond chain 1 res 1 seqnum 1 inscode 1 atname 1 chain 2 res 2 seqnum 2 inscode 2 atname 2 dist molecule id chain_id class symop symop no cell_i cell j cell k rxx rxy rxz tx Chapter 13 Scheme Scripting Functions 201 ryx ryy ryz ty rzx rzy rzz tz int_natoms int_nres int area int_solv_en pvalue residues residue ser no name seq num ins code bonds asa bsa solv en 13 37 coot utils annotations procedure 3D annotations a bit of a hack currently default ball and st
216. m the menus File gt Save Coordinates you are first presented with a list of molecules which have coordinates As well as the molecule number there is the molecule name very frequently the name of the file that was read in to generate the coordinates in coot initially However this is only a molecule name and should not be confused with the filename to which the coordinates are saved The coordinates filename can be selected using the Select Filename button If your filename ends in cif mmcif or mmCIF then an mmCIF file will be written not a PDB file 4 9 Setting the Space Group If for some reason the pdb file that you read does not have a space group or has the wrong space group then you can set it using the following function set space group imol symbol e g set space group 0 P 41 21 2 4 10 Anisotropic Atoms By default anisotropic atom information is not represented To turn them on use Draw gt Anisotropic Atoms gt Show Anisotropic Atoms gt Yes or the command set show aniso 1 You cannot currently display thermal ellipsoids for isotropic atoms 4 11 Symmetry Coordinates symmetry is dynamic Symmetry atoms can be labeled Every time you recentre the symmetry coordinates are updated The information shown contains the atom information and the symmetry operation number and translations needed to generate the atom in that position By default symmetry atoms are not displaye
217. map number and a weighting factor 1 0 in this case 6 11 Map Sampling By default the Shannon sampling factor is the conventional 1 5 Use larger values Edit gt Map Parameters gt Sampling Rate for smoother maps This value can be set by the scripting command set map sampling rate 2 5 6 12 Dragged Map By default the map is re contoured at every frame during a drag Ctrl Left mouse Some times this can be annoyingly slow and jerky so it is possible to turn it off Draw gt Dragged Map gt No To change this by scripting set active map drag flag 0 6 13 Dynamic Map Sampling and Display Size If activated Edit gt Map Parameters gt Dynamic Map Sampling the map will be re sampled on a more coarse grid when the view is zoomed out If Display Size is also activated the box of electron density will be increased in size also In this way you can see electron density for big maps many unit cells and the graphics still remain rotatable D Jan Dohnalek for instance T a value of 2 5 is often sufficient Chapter 6 Map Related Features 92 If you want to have these functions active for all maps add the following to your initial ization file Section 3 10 2 Scheme page 12 set dynamic map sampling on set dynamic map size display on 6 14 Skeletonization The skeleton also known as Bones can be displayed for any map A map can be skeletonized using Calculate gt Map Skeleton U
218. may want to know the space group of a particular molecule Interactively for maps you can see it using the Map Properties button in the Molecule Display Control dialog There is a scripting interface function that returns the space group for a given molecule show spacegroup imol You can force a space group onto a molecule using the following set space group imol space group where space group is one of the standard CCP4 space group names e g P 21 21 21 To show the symmetry operators of a particular molecule use get symmetry imol which will return a list of strings 3 14 Recentring View e Use Control left mouse to drag around the view e Or e middle mouse over an atom In this case you will often see slide recentring the graphics smoothly changes between the current centre and the newly selected centre e or e Use Draw gt Go To Atom to select an atom using the keyboard Note that you can subsequently use Space in the graphics window OpenGL canvas to recentre on the next Ca e or e To centre on an arbitrary position x y z use the scripting function set rotation centre x y z e or e Use the keyboard Ctrl G then key in a residue number and optionally a chainid and press Return If you don t want smooth recentring sliding Edit gt Preferences gt Smooth Recentring gt Off You can also use this dialog to speed it up a bit by decreasing the number of steps inste
219. med view remove named view view name function Where view_name is a string the view with the given name 11 58 4 remove view remove view view number function Where view_number is an integer number the given view number Chapter 11 Scripting Functions 11 58 5 add view description add view description view_number description Where e view_number is an integer number e description is a string Add a view description annotation to the give view number 11 58 6 add action view add action view view name action function Where e view name is a string e action function is a string add a view not add to an existing view that does something e g undisplays a molecule rather than move the graphics Returns the view number for this new view 11 58 7 insert action view after view insert action view after view view number view name action function Where e view number is an integer number e view name is a string e action function is a string add an action view after the view of the given view number Returns the view number for this new view 11 58 8 save views Save views view file name Where view filename is a string save views to view file name 11 58 9 clear all views clear all views Clear the view list 11 59 Background Colour 133 function function displays or function function function Chapter 11 Scripting Functions 134 11 59 1 set background colo
220. mm why make a side effect like that Why not return coot listener socket so that the caller can set it There may be a reason And the reason is that I can then call coot listener idle function proc without having to use a c variable open coot listener socket with timeout port number host name procedure yet another go to make a coot port reader work This time we use a gtk timer to read stuff from the socket The gtk timer function must return 1 to be called again When we want to close the socket reader simply make the function return 0 coot socket timeout func procedure based on coot listener idle function proc coot listener idle function proc procedure Do this thing when idle currently set to listen to the coot listener socket eval socket string s procedure the function to run from the main thread to evaluate a string 13 34 coot probe command procedure This is full pathname of molprobity s probe program reduce command procedure This is full pathname of molprobity s reduce program do coot tips flag procedure This has be be here in a general place because tips gui where it used to be is conditionally loaded default to tips gui displayed is true load all scheme procedure Note the position of coot gui is important It seem that if there are too many files in front of it even blank ones coot barfs when it gets to coot gui scm 20060203 I have now enabled coot in scripting mode
221. model number 177 11 108 2 single model view this model number 177 11 108 3 single model view next model number 177 11 108 4 single model view prev model number 177 11 109 graphics 2D ligand view 178 11 109 1 set show graphics ligand view 2000 eeee 178 11 110 Sectionless Tunctionsg 0 00 cece eee eee eee 178 11 110 1 get write conect record state 6 0 cee eee eee 178 11 110 2 set write conect record state 0 e eee eee eee 178 11 110 3 make and draw patterson 00 eee eee ee eee 178 xxi 12 More Scripting Functions 179 12 1 More Symmetry Functions 0 0 0 e cece eee ee 179 12 1 1 dget symmelry seeker eG nies ee EY 179 12 2 Extra Map Functions ee 179 12 2 1 map colour componente ee 179 12 3 Multi Residue Torsion ssssseseeeeess eh 179 12 3 1 maulti residue torsion fit scm 0 cece eee eee eee 179 12 4 Execute Refmac 0 cece eee n nnn nnn 179 12 4 1 execute refmac real 0 cece eee eens 179 12 5 Dictionary Functions 0 180 12 5 1 dictionaries read 2 00 cece eee eee nee eee 180 12 6 Restraints Interface 180 12 6 1 set monomer restraints 0 00 eee eee 180 12 7 Atom Information functions 0 cece eee eee 180 12 7 1 residue info ccc en 181 1272 add miolecules 5 2 eR a 181 12 7 3 chear and update molecule 0 cece eee ee
222. n 46 5 42 Refine All Waterg eee eee me 46 5 43 Moving Molecules Ligands AN gg E sete Mate aa 46 5 44 Modifying the Labels on the Model Fit Refine dialog 47 Map Related Features 48 6 1 Maps mm General sorer gedet cad ia br hg yere 48 6 1 1 Map Reading Bus 48 6 2 Create a Man tesis ssni gere EEN ei d ds 48 6 2 1 Auto read MTZ nie 48 6 2 2 Reading CTE data ze an eR RR cela hat 48 6 2 3 Reading PHS data 49 6 3 Map Contouring soos aa o dl ba Se 49 6 4 Map Extendida ati ene ti OE eG breue ene ed 50 6 5 Map Contour Scrolling L mts erasan 50 6 6 Map Line Width sens 50 6 7 Dynamic Map colouring 06 cece eee eee eee ee 50 6 8 Difference Map Colouring 00 e cece eee ee eens 51 6 9 Make a Difference Map 51 6 10 Make an Averaged Man 51 DER Map Sampling 9 scented Ace bie READER sae ae 51 6 12 Dragged Map ENEE doesn RE RA RO Reds 51 6 13 Dynamic Map Sampling and Display Size 51 6 14 Hkeletonisat on eS mh e m rn 52 6 15 Map Sharpening cece cece nne 52 6 16 PatlersoHso uc A a AE e 52 0T C C MaSES So ede eto ee t i S euet 52 Gal Gl Example o mu deeds 53 618 Trimmings eee daa ce em ker eRR Oe RU DONO RETE 93 6 19 Map Transformation eseis srs rara ccc ccc cece e 53 6 20 EXport Map sr oes rt le la ache tail 54 T Validator dis des 55 7 1 Ramachandran Dlots 0 0 ccc cece cece cee aes
223. n page 52 When three or more atoms have been built in a chain Coot will use a prior probability distribution for the next position based on the position of the previous three The analysis is similar to that of Oldfield amp Hubbard 1994 however it is based on a more recent and considerably larger database Little crosses are drawn representing directions in which is is possible that the chain goes and a baton is drawn from the current point to one of these new positions If you don t like this particular direction use Try Another The list of directions is scored according to the above criterion and sorted so that the most likely is at the top of the list and displayed first as the baton direction When starting baton building be sure to be about 3 8 from the position of the first placed Ca this is because the next Ca is placed at the end of the baton the baton root being at the centre of the screen So when trying to baton build a chain starting at residue 1 centre the screen at about the position of residue 2 It seems like a good idea to increase the map sampling to 2 or even 2 5 before reading in your mtz file a grid sampling of about 0 5 seems reasonable when trying to baton build a low resolution map You can set the map sampling using Edit Map Parameters gt Map Sampling T J Oldfield amp R E Hubbard 1994 Analysis of Ca Geometry in Protein Structures Proteins Structure Function and Genetics 18
224. nction Where e f isa number e f2 is a number e f2 is a number set the colour of the last highest molecule number map 11 15 12 set map colour set map colour imol red green blue function Where e mol is an integer number e red is a number e green is a number e blue is a number set the colour of the imolth map 11 15 13 set last map sigma step set last map sigma step f function Where f is a number set the sigma step of the last map to f sigma Chapter 11 Scripting Functions 11 15 14 set contour by sigma step by mol set contour by sigma step by mol fstate imol function Where e fisa number e state is an integer number e imolis an integer number set the contour level step set the contour level step of molecule number imol to f and variable state setting state to 0 turns off contouring by sigma level 11 15 15 data resolution data resolution imol function Where mol is an integer number return the resolution of the data for molecule number imol Return negative number on error otherwise resolution in A eg 2 0 11 15 16 model resolution model resolution imol function Where mol is an integer number return the resolution set in the header of the model coordinates file If this number is not available return a number less than 0 11 15 17 export map export map imol filename function Where e imolis an integer number e filename is a string export write to disk the map of molecul
225. nction Where e imol is an integer number e filename is a string save coordinates of molecule number imol in filename Returns status 1 is good success 0 is fail Chapter 11 Scripting Functions 111 11 35 Read Phases File Functions 11 35 1 read phs and coords and make map read phs and coords and make map pdb filename function Where pdb filename is a string read phs file use coords to get cell and symm to make map uses pending data to make the map 11 35 2 read phs and make map using cell symm from previous mol read phs and make map using cell symm from previous mol function phs filename Where phs filename is a string read a phs file the cell and symm information is from previously read most recently read coordinates file For use with phs data filename provided on the command line 11 35 3 read phs and make map using cell symm from mol read phs and make map using cell symm from mol phs filename function imol Where e phs filename is a string e imolis an integer number read phs file and use a previously read molecule to provide the cell and symmetry information Returns the new molecule number return 1 if problem creating the map e g not phs data file not found etc 11 35 4 read phs and make map using cell symm read phs and make map using cell symm phs_file name function hm spacegroup a b c alpha beta gamma Where e phs file name is a string e hm spacegroup is a string e ais a number
226. nction recentre_on_read_pdb_flag Where e filename is a string e recentre_on_read_pdb_flag is an integer number read coordinates from filename with option to not recentre set recentre on read pdb flag to 0 if you don t want the view to recentre on the new coordinates 11 8 16 handle read draw molecule and move molecule here handle read draw molecule and move molecule here filename function Where filename is a string read coordinates from filename and recentre the new molecule at the screen rotation centre 11 8 17 read pdb read pdb filename function Where filename is a string read coordinates from filename 11 8 18 assign hetatms assign hetatms imol function Where mol is an integer number some programs produce PDB files with ATOMs where there should be HETATMs This is a function to assign HETATMs as per the PDB definition 11 8 19 hetify residue hetify residue imol chain id resno ins_code function Where e imolis an integer number e chain id is a string e resno is an integer number e ins_code is a string if this is not a standard group then turn the atoms to HETATMs Return 1 on atoms changes 0 on not Return 1 if residue not found Chapter 11 Scripting Functions 11 8 20 residue has hetatms residue has hetatms imol chain_id resno ins_code function Where e imol is an integer number e chain d is a string e resno is an integer number e ins code is a string residue has HETATMs
227. nctions 11 50 1 handle cns data file handle cns data file filename imol Where filename is a string imol is an integer number read CNS data currently only a placeholder 11 50 2 handle cns data file with cell handle cns data file with cell filename imol a b c alpha beta gamma spg_info Where filename is a string imol is an integer number is a number b is a number c is a number alpha is a number beta is a number gamma is a number spg info is a string read CNS data currently only a placeholder 128 function function a b c are in Angstroems alpha beta gamma are in degrees spg is the space group info either delimited symmetry operators or the space group name 11 51 mmCIF Functions 11 51 1 open cif dictionary file selector dialog open cif dictionary file selector dialog open the cif dictionary file selector dialog 11 52 SHELXL Functions 11 52 1 read shelx ins file read shelx ins file filename recentre flag Where e filename is a string e recentre flag is an integer number read a SHELXL ins file function function Chapter 11 Scripting Functions 129 11 52 2 write shelx ins file write shelx ins file imol filename function Where e imol is an integer number e filename is a string write a SHELXL ins file for molecule number imol 11 53 Validation Functions 11 53 1 difference map peaks difference map peaks imol imol_coords level max
228. ndran plot background block size blocksize function Where blocksize is a number set the ramachandran plot background block size Smaller is smoother but slower Should be divisible exactly into 360 Default value is 10 11 54 5 ramachandran plot differences ramachandran plot differences imoll imol2 function Where e imoll is an integer number e imol2 is an integer number 2 molecule ramachandran plot NCS differences a k a A Kleywegt Plot 11 54 6 ramachandran plot differences by chain ramachandran plot differences by chain imoll imol2 a chain function b_chain Where e imoll is an integer number e imol2 is an integer number e a_chain is a string e b chain is a string A chain specific Kleywegt Plot 11 55 Sequence View Interface 11 55 1 do sequence view do sequence view imol function Where mol is an integer number display the sequence view dialog for molecule number imol Chapter 11 Scripting Functions 11 56 Atom Labelling 11 56 1 set brief atom labels set brief atom labels istat Where istat is an integer number use brief atom names for on screen labels call with istat 1 to use brief labels istat 0 for normal labels 11 56 2 brief atom labels state brief atom labels state the brief atom label state 11 57 Screen Rotation 11 57 1 rotate y scene rotate y scene nsteps stepsize Where e nsteps is an integer number e stepsize is a number rotate view round y axis stepsize degrees for n
229. ng attribute 109 set auto fit best rotamer clash flag 148 set auto read column labels 91 set auto read do difference map too 91 set b factor bonds scale factor 140 Set background colour sss 134 set backup compress files 83 Set baton build params 152 set baton mode cesses 151 set bond thickness 00000 138 set bond thickness intermediate atoms 138 set brief atom labels sss 131 set browser interface sss 167 set button label for external refinement A A ee 174 set colour by chain ee 102 Set colour Dy nolecule 103 set colour map rotation for map 103 set colour map rotation on read pdb 102 set colour map rotation on read pdb c only ELAR ab Mier e Senses Uie 102 set colour map rotation on read pdb flag words EENEG 102 set console display commands hilights 100 set console display commands state 100 set contour by sigma step by mol 86 set control key for rotate 80 set convert to v2 atom names 73 set default bond thicknesS 138 set default initial contour level for difference map vic Seri 77 set default initial contour level for map EE 77 set default representation type 138 set default temperature factor for new ATOMS e sec ug Id she Reng Lucetius eod 108 set delete dialog position
230. ngle factor state ooooooommmo o o 105 11 27 11 set model fit refine dialog positi0M 0oooooomm m 105 11 27 12 set display control dialog position 105 11 27 13 set go to atom window position oooccoorcccooo 105 11 27 14 set delete dialog position ssssususus nrun n nnn 105 11 27 15 set rotate translate dialog position 0 o ooo 106 11 27 16 set accept reject dialog positi0M ooooooooommo 106 11 27 17 set ramachandran plot dialog position 106 11 27 18 set edit chi angles dialog position 106 11 27 19 set rotamer selection dialog position 106 11 28 Smooth Scrolling isea r eee erre 107 11 28 1 set smooth scroll flag 0 0 cee eee 107 11 28 2 get smooth scroll 0 0 cece ene eee 107 11 28 3 set smooth scroll steps 00 c cece cence ee eee 107 11 28 4 set smooth scroll limit 0 00 e eee eee 107 11 29 Font ise in ld ty ey Lobe cae Gee a eee 107 ILR Set font siZ065 fiat ren web E Od dna 107 11 29 2 set Font aze en 107 11 29 3 set Font colour een 107 11 30 Rotation Centre ce eet ER xa EN 108 1T 30 T go to ligand ee benc cei peut e ep bene e 108 11 31 Atom Selection Uulues cece eee 108 11 31 1 clear pend ng nicka 0 0 cece eee eee eens 108 xii 11 31 2 set default temperature factor for new atoms 108 11 31 3 default new atoms b factor 0 00 cece
231. no graphics no graphics com mand line option In that case we need to not load up scheme files which load up gtk currently coot gui and tips gui Chapter 13 Scheme Scripting Functions 200 13 35 hello first non trivial name procedure Primarily for Indian Names Say we are given str list M D Albert Dorkins We want to return Albert not M We reject names that are one character long and names that are 2 characters long that end in So M is rejected but Ma is not An excercise for the committed is to also reject run together dotted initials such as D K I was sufficiently committed 13 36 parse pisa xml pisa command procedure define pisa command home paule ccp4 ccp4 6 1 2 bin pisa pisa assemblies xml imol file name procedure it calls parse pisa assemblies which does the work pisa handle sxml molecule imol molecule pisa results type procedure a interface molecule record contains information about pvalue and residues parse pisa assemblies procedure pisa assemblies pisa_results name status total asm asm_set ser no assembly id size mmsize diss_energy asa bas entropy diss area int energy n uc n diss symNumber molecule chain_id rxx rxy rxz tx ryx ryy ryz ty rzx rzy rzz tz rxx f rxy f rxz f tx f ryx f ryy f ryz f ty f rzx f rzy f rzz f tz f prep for pisa mode imol procedure 20100213 prep for pisa needs to make directory config file write the pdb file and thre return va
232. nt map function the molecule number of the map used for refinement Returns the map number if it has been set or there is only one map return 1 on no map set ambiguous or no maps 11 43 30 set imol refinement map set imol refinement map imol function Where mol is an integer number set the molecule number of the map to be used for refinement fitting Returns imol on success 1 on failure 11 43 31 does residue exist p does residue exist p imol chain_id resno inscode function Where e imolis an integer number e chain_id is a string e resno is an integer number e inscode is a string Does the residue exist Raw function Returns 0 on not exist 1 on does exist Chapter 11 Scripting Functions 124 11 43 32 add extra bond restraint add extra bond restraint imol chain_id_1 res_no_1 ins_code 1 function atom_name_1 alt_conf_1 chain_id_2 res_no_2 ins code_2 atom name 2 alt_conf_2 bond_dist esd Where e mol is an integer number e chain_id_1 is a string e res no 1 is an integer number e ins code IJ is a string e atom mname 1 is a string e alt_conf_1 is a string e chain id 2 is a string e res_no_2 is an integer number e ins code 2 is a string e atom name 2 is a string e alt_conf_2 is a string e bond_dist is a number e esd is a number add a user define bond restraint this extra restraint is used when the given atoms are selected in refinement or regu larization Returns the
233. nteger number e istat is an integer number set the hydrogen drawing state istat 0 is hydrogens off istat 1 show hydrogens 11 62 8 draw hydrogens state draw hydrogens state imol function Where mol is an integer number the state of draw hydrogens for molecule number imol return 1 on bad imol 11 62 9 graphics to ca representation graphics to ca representation imol function Where mol is an integer number draw molecule number imol as CAs 11 62 10 graphics to ca plus ligands representation graphics to ca plus ligands representation imol function Where mol is an integer number draw molecule number imol as CA ligands 11 62 11 graphics to bonds no waters representation graphics to bonds no waters representation imol function Where mol is an integer number draw molecule number imol with no waters 11 62 12 graphics to bonds representation graphics to bonds representation mol function Where mol is an integer number draw molecule number imol with normal bonds Chapter 11 Scripting Functions 140 11 62 13 graphics to ca plus ligands sec struct representation graphics to ca plus ligands sec struct representation mol function Where mol is an integer number draw molecule number imol with CA bonds in secondary structure representation and ligands 11 62 14 graphics to sec struct bonds representation graphics to sec struct bonds representation imol function Where mol is an integer number
234. nusunusu unenee 141 11 62 24 additional representation by string 141 11 62 25 additional representation by attributes 141 11 68 Dots Representation 0 0 cece eee ene eee eee 142 11 68 1 dots aca oh ad eee ita RR ee 142 11 63 2 set dots colour 0 cece eee eee een nes 142 11 63 38 unset dots colour 0 00 c cece eee eee ees 142 11 63 4 elear dete cocineta ri eb EE Rs 143 11 63 5 clear dots bn name cece eee eee eens 143 11 03 6 let get re as 143 11 64 Pep flip Interface 143 R NNEN 143 11 65 Rigid Body Refinement Interface 143 11 65 1 rigid body refine zone 0 6 c eee eee eens 143 11 65 2 set rigid body fit acceptable fit fraction 144 11 66 Add Terminal Residue Functions eee 144 11 66 1 set add terminal residue immediate addition 144 11 66 2 add terminal residue 0 00 cece eee eee eee 144 11 66 3 add terminal residue using phi psi suse 144 11 66 4 set add terminal residue default residue type 145 11 66 5 set add terminal residue do post refine 145 11 66 6 add terminal residue do post refine state 145 11 67 Delete Residues ene ened 145 11 67 1 delete reidue range ccc cece eee eee eee 145 11 67 2 delete residue 0 e cece enerne rrer 145 11 67 38 delete residue with full spec 0 e eee eee eee 146 11 67 4 delete residue hydrogens
235. o ligand stop This was designed to create an NCS copy of a ligand or range of residues in the active site of one chain to the as yet unoccupied active site of another i e it makes a NCS ligand D 1 that is a NCS copy of ligand C 1 using an NCS operator that maps protein chain A onto chain B Chapter 13 Scheme Scripting Functions 192 13 13 shelx shelxl refine procedure shelxl refine primitive procedure hkl file in can be null or list astring read shelx lst file procedure ie create a interesting things GUI for split and other things in a shelx Jet file 13 14 what check strip leading spaces str procedure 53 gt 53 now I un go to residue by spec imol spec procedure consider for coot utils residue spec gt string spec procedure consider for coot utils get flip residue line procedure make this internal where line is something like 53 HIS 53 A12 ignore xxxxI Cyy xxxx is 4char resno I insertion code C chain id yy is model number return a residue spec or f problem residues gt dialog imol problemed res list list procedure A problemed res list is improper pair where the car is a pair of string one describing the problem and the other being the fix it button label The cdr is a list of residue specs A problemed flip list list is a list of those things parse check db imol file name action procedure action is either gui then we get a gui or apply actions then the
236. oarding 2 Mousing and Keyboarding How do we move around and select things Left mouse Drag Rotate view Ctrl Left Mouse Drag Translates view Shift Left Mouse Label Atom Right Mouse Drag Zoom in and out Ctrl Shift Right Mouse Drag Rotate View around Screen Z axis Middle mouse Centre on atom Scroll wheel Forward Increase map contour level Scroll wheel Backward Decrease map contour level See also Chapter Chapter 9 Hints and Usage Tips page 60 for more help 2 1 Next Residue pace Next Residue Shift Space Previous Residue See also Recentring View Section Section 3 14 Recentring View page 15 2 2 Keyboard Contouring Use or on the keyboard if you don t have a scroll wheel 2 3 Mouse Z Translation and Clipping Here we can change the clipping and Translate in Screen Z Ctrl Right Mouse Drag Up Down changes the slab clipping planes Ctrl Right Mouse Drag Left Right translates the view in screen Z Chapter 2 Mousing and Keyboarding 6 2 4 Keyboard Translation Keypad 3 Push View Z translation Keypad Pull View Z translation 2 5 Keyboard Zoom and Clip Zoom out N M Zoom in D Slim clip F Fatten clip 2 6 Scrollwheel When there is no map using the scroll wheel has no effect If there is exactly one map displayed the scroll wheel will change the contour level of that map If there are two or more maps the map for which the contour level is changed can
237. ode for rotation Prefered by some including Dirk Kostrewa I don t think this mode works properly yet 11 10 2 control key for rotate state control key for rotate state function return the control key rotate state 11 10 3 blob under pointer to screen centre blob under pointer to screen centre function Put the blob under the cursor to the screen centre Check only positive blobs Useful function if bound to a key The refinement map must be set We can t check all maps because they are not or may not be on the same scale Returns 1 if successfully found a blob and moved there return 0 if no move 11 11 Cursor Function 11 11 1 set pick cursor index set pick cursor index icursor index function Where icursor_index is an integer number let the user have a different pick cursor sometimes the default GDK_CROSSHATIR is hard to see let the user set their own Chapter 11 Scripting Functions sl 11 12 Model Fit Refine Functions 11 12 1 post model fit refine dialog post model fit refine dialog function display the Model Fit Refine dialog 11 12 2 show select map dialog show select map dialog function display the Display Manager dialog 11 12 3 set model fit refine rotate translate zone label set model fit refine rotate translate zone label txt function Where txt is a string Allow the changing of Model Fit Refine button label from Rotate Translate Zone 11 12 4 set model fit refine place atom at po
238. odel molecule is analysed 7 3 Chiral Volumes The dictionary is used to identify the chiral atoms of each of the model s residues A clickable list is created of atoms whose chiral volume in the model is of a different sign to that in the dictionary During refinement and regularization Coot will pop up dialogs warning about chiral volume errors if you have them This can be annoying You can inhibit this dialog like this set show chiral volume errors dialog 0 the not GLY or PRO is the most familiar Ramachandran plot 2 prolines have a grey outline rather than a black one triangles are glycines 3 but that s partly the idea I suppose Chapter 7 Validation 56 7 3 1 Fixing Chiral Volume Errors There are two obvious ways 1 mutate and auto fit rotamer mutate it to the residue type that it is 2 RS Refine the residue and invert the chiral centre by pulling an atom Usually you can pull the CA to the other side of the plane made by the chiral neighbouring atoms using ctrl left click Sometimes giving the CB a good old tweak is the easier way Inverting the CB of THR is easier just move the OG so that the plane of the neighbours is on the other side of the CB again with ctrl left click 7 4 Blobs a k a Unmodelled density This is an interface to the Blobs dialog A map and a set of coordinates that model the protein are required A blob is region of relatively high residual election density that cannot be explain
239. of the screen 11 62 22 make ball and stick make ball and stick mol atom_selection_str bond_thickness sphere_size function do spheres flag Where e imolis an integer number e atom selection str is a string e bond thickness is a number e sphere size is a number e do spheres flag is an integer number make a ball and stick representation of imol given atom selection e g make ball and stick 0 1 0 15 0 25 1 11 62 23 clear ball and stick clear ball and stick imol function Where mol is an integer number clear ball and stick representation of molecule number imol 11 62 24 additional representation by string additional representation by string imol atom selection function representation type bonds box type bond_width draw hydrogens flag Where e imolis an integer number e atom selection is a string e representation type is an integer number e bonds boz type is an integer number e bond_width is a number e draw hydrogens flag is an integer number return the index of the additional representation Return 1 on error 11 62 25 additional representation by attributes additional representation by attributes imol chain id function resno_start resno end ins_code representation type bonds box type bond width draw hydrogens flag Where e imolis an integer number Chapter 11 Scripting Functions 142 e chain_id is a string e resno_start is an integer number e resno_end is an integer number e ins
240. ol function Where mol is an integer number return the symmetry of the imolth molecule Return as a list of strings the symmetry operators of the given molecule If imol is a not a valid molecule return an empty list 12 2 Extra Map Functions 12 2 1 map colour components map colour components imol function Where mol is an integer number return the colour triple of the imolth map e g list 0 4 0 6 0 8 If invalid imol return scheme false 12 3 Multi Residue Torsion 12 3 1 multi residue torsion fit scm multi residue torsion fit scm imol residues specs scm function Where e imolis an integer number e residues specs scm is a SCM fit residues note fit to the current refinement map 12 4 Execute Refmac 12 4 1 execute refmac real execute refmac real pdb in filename pdb out filename mtz_in_filename function mtz out filename cif lib filename fobs col name sigfobs col name r free col name have sensible free r flag make molecules flag refmac count string swap map colours post refmac flag imol refmac map diff map flag phase combine flag phib_string fom string ccp4i project dir Where e pdb in filename is a std string e pdb out filename is a std string Chapter 12 More Scripting Functions 180 mtz_in_filename is a std string mtz_out_filename is a std string cif lib filename is a std string fobs_col_name is a std string sigfobs_col_name is a std string r_free_col_name is
241. olbar hide main toolbar function hide the horizontal main toolbar in the GTK2 version 11 9 15 show main toolbar show main toolbar function show the horizontal main toolbar in the GTK2 version the toolbar is shown by default 11 9 16 show model toolbar all icons show model toolbar all icons function show all available icons in the modelling toolbar same as MFR dialog 11 9 17 show model toolbar main icons show model toolbar main icons function show only a selection of icons in the modelling toolbar 11 9 18 reattach modelling toolbar reattach modelling toolbar function reattach the modelling toolbar to the last attached position 11 9 19 set model toolbar docked position set model toolbar docked position s ate function Where state is an integer number to swap sides of the Model Fit Refine toolbar 0 default is right 1 is left 2 is top 3 is bottom Chapter 11 Scripting Functions 11 9 20 suck model fit dialog suck model fit dialog function reparent the Model Fit Refine dialog so that it becomes part of the main window next to the GL graphics context 11 9 21 add status bar text add status bar text s function Where s is a string Put text s into the status bar use this to put info for the user in the statusbar less intrusive than popup 11 10 Mouse Buttons 11 10 1 set control key for rotate set control key for rotate state function Where state is an integer number Alternate m
242. olithic version e http www biop ox ac uk coot doc chapters user manual toc html which is split into sections In the Menu item About under Online Docs URL there is a entry bar that can be used to search the Coot documentation via Google The results are returned as a web page in web browser The browser type can be specified as in this example set browser interface firefox Example usage can be found in xxx share coot scheme group settings scm 9 2 Low Resolution Building structures using low resolution data is a pain We hope to make it less of a pain in future but there are some things that you can do now e Add Planar Peptide Restraints Add restraints via scripting command e Use Secondary Structure Restraints where appropriate under Refinement Control e Check Chirals Check Chiral Volumes regularly e Change the Weighing Scheme set matrix 20 0 Default is 60 the lower the number the more the geometry is idealised 9 3 Coot Droppings This describes the files and directory that coot leaves behind after it has been fed sorry I mean used Everything except the O coot state scm state file can comfortably be deleted if needed after coot has finished You can stop the state and history files being written if you start coot with the no guano option e O coot state scm The most important file This contains the state of coot when you last exited It contains things like which molecules were
243. om a residue serial number Returns NULL scheme False on failure Chapter 11 Scripting Functions 11 6 3 seqnum from serial number seqnum from serial number imol chain_id serial num function Where e imolis an integer number e chain id is a string e serial num is an integer number a residue seqnum normal residue number from a residue serial number Returns 9999 on failure 11 6 4 insertion code from serial number insertion code from serial number mol chain jd serial num function Where e imolis an integer number e chain id is a string e serial num is an integer number the insertion code of the residue Returns NULL scheme False on failure 11 6 5 n models n models imol function Where mol is an integer number the chain_id string of the ichain th chain molecule number imol return the number of models in molecule number imoluseful for NMR or other such multi model molecules return the number of models or 1 if there was a problem with the given molecule Returns the chain id 11 6 6 n chains n chains imol function Where mol is an integer number number of chains in molecule number imol Returns the number of chains 11 6 7 is solvent chain p is solvent chain p imol chain id function Where e imolis an integer number e chain id is a string Chapter 11 Scripting Functions is this a solvent chain Raw function This is a raw interface function you should gener
244. om window on changed mol imol function Where mol is an integer number update the Go To Atom window 11 37 7 update go to atom window on new mol update go to atom window on new mol function update the Go To Atom window This updates the option menu for the molecules 11 37 8 set go to atom molecule set go to atom molecule imol function Where mol is an integer number set the molecule for the Go To Atom For dynarama callback sake The widget class knows which molecule that it was generated from so in order to go to the molecule from dynarama we first need to the the molecule because does not mention the molecule see Next Previous Residue for reasons for that This function simply calls the graphics info t function of the same name Also used in scripting where go to atom chain residue atom name does not mention the molecule number 20090914 PE set go to atom molecule can be used in a script and it should change the go to atom molecule in the Go To Atom dialog if it is being displayed This does mean of course that using the ramachandran plot to centre on atoms will change the Go To Atom dialog Maybe that is surprising maybe not 11 38 Map and Molecule Control 11 38 1 post display control window post display control window function display the Display Constrol window Chapter 11 Scripting Functions 115 11 38 2 set map displayed set map displayed imol state function Where e mol is an integer number
245. oms sssessseeeee eee 173 11 96 Partial Charges 173 11 96 1 sbhow partialcharge mfo 0 0 cece eee eee 173 11 97 EM mterface cii e eugene Ose Pa eae etn teens 173 E HE scale Cll A A A 173 11 98 CCP4mg Interface 174 11 98 1 write ccp4mg picture description oooocccocooccoc 174 11 98 2 get atom colour from mol no sssssssessseses nenea 174 11 99 Aux functions ssssssssssssssssses en 174 11 99 1 Laplace A 174 117100 SMILES cuotas aa 174 11 100 1 do smiles gui lesse 174 11 101 PHENIX Support 174 11 101 1 set button label for external refinement 174 11 102 Graphics lest 174 11 102 1 place text cssc Rma c RR ere Ker 174 11 102 2 r move text ccccemeence me e ee eee RD 175 11 102 3 Lest Andes near position 0 00 cece eee ee eee 175 11 103 PISA Interaction ssseseeese nee eens 175 11 103 1 pisa interaction cesses 175 TAON LS e EA uberem Deer Se 175 11 104 1 fit to map by random jiggle nssssnsese nenna 175 11 105 SBase interface 0 cee eee eee eee 176 11 105 1 get sbase monomer 0 0 c eee eee eee ees 176 T1 106 ELE VIewi epson Sade Sas Pek a a open 176 11 106 1 fle view set water dist Max 00 cece eee eee eee 176 11 106 2 De view set h bond dstmgs 000 eee aee 176 11107 LSQ improve coy oe o ee pene ba Sea ed 176 11 107 1 Isq improve s 20 5 e ks Rm da ra 176 11 108 single model wien 177 11 108 1 single model view
246. on the molecule number and a user settable parameter e set colour map rotation on read pdb 30 The default value is 31 Also one is able to select only the Carbon atoms to change colour in this manner set colour map rotation on read pdb c only flag 1 The colour map rotation can be set individually for each molecule by using the GUI Edit gt Bond Colours 1 Hue Saturation Value Intensity Chapter 4 Coordinate Related Features 20 4 5 Bond Parameters The various bond parameters can be set using the GUI dialog Draw gt Bond Parameters or via scripting functions The represention style of the molecule that has the active residue if any can be changed using the scroll wheel with Ctrl and Shift 4 5 1 Bond Thickness The thickness width of bonds of individual molecules can be changed This can be done via the Bond Parameters dialog or the scripting interface set bond thickness thickness imol where imol is the molecule number The default thickness is 3 pixels The bond thickness also applies to the symmetry atoms of the molecule The default bond thickness for new molecules can be set using set default bond thickness thick where thick is an integer There is no means to change the bond thickness of a residue selection within a molecule 4 5 2 Display Hydrogens Initially hydrogens are displayed They can be undisplayed using set draw hydrogens mol no 0 where mol no is the molecule number Th
247. or a particular molecule imol and dots set identifier dots handle clear dots imol dots handle There is a function to return how many dots sets there are for a particular molecule imol n dots set imol 4 18 Ball and Stick Representation Fragments of the molecule can be rendered as a ball and stick molecule make ball and stick imol atom selection bond thickness sphere size draw spheres flag e g make ball and stick 0 1 A 10 20 0 3 0 4 1 The ball and stick representation can be cleared using clear ball and stick imol 4 19 Mean Median Temperature Factors Coot can be used to calculate the mean average and median temperatures factors average temperature factor imol median temperature factor imol 1 is returned if there was a problem 4 20 Secondary Structure Matching SSM The excellent SSM alogrithm of Eugene Krissinel is available in Coot The GUI interface is straight forward and can be found under Calculate SSM Superpose You can specify the specific chains that you wish to match using the Use Specific Chain check button There is a scripting level function which gives even finer control superpose with atom selection imo11 imol2 mmdb atom selection string 1 mmdb atom selection string 2 move copy flag the move copy flag should be 1 if you want to apply the transformation to a copy of imol2 rather than imol2 itself Otherwise move copy flag should be 0 mmdb atom selection str
248. orks nicely and gives a better image than using Coot s built in antialiasing Also for nVidia graphics card users there is the application nvidia settings Antialiasing Setting gt Override Application Settings and slide the slider to the right On restarting Coot it should be in antialias mode 3 3 Molecule Number Coot is based on the concept of molecules Maps and coordinates are different represen tations of molecules The access to the molecule is via the molecule number It is often important therefore to know the molecule number of a particular molecule The Molecule Number of a molecule can be found by clicking on an atom of that molecule if it has coordinates of course The first number in brackets in the resulting text in the status bar and console is the Molecule Number The Molecule Number can also be found in Display Control window Section Section 3 7 Display Manager page 10 It is also displayed on the left hand side of the molecule name in the option menus of the Save Coordinates and Go To Atom windows l Put your mouse over a widget for a couple of seconds if that widget has a tooltip it will pop up in yellow box or a grey box for some reason if you are using Macintosh that works for me at least Chapter 3 General Features 9 3 4 Display Issues The graphics window is drawn using OpenGL It is considerably smoother i e more frames sec when using a 3D accelerated X server Th
249. other atoms in the structure are in sensible positions If they are then it is sensible not to put this residue too close to them if they are not then there should be no restriction from the other atoms as to the position of this residue the default is are sensible which means that the algorithm is prevented from finding solutions that are too close to the atoms of other residues set rotamer check clashes 0 will stop this There is a scripting interface to auto fitting rotamers auto fit best rotamer resno alt loc ins code chain id imol coords imol map clash flag lowest rotamer probability where resno is the residue number alt loc is the alternate alternative location symbol e g A or B but most often ins code is the insertion code usually imol coords is the molecule number of the coordinates molecule imol map is the molecule number of the map to which you wish to fit the side chains 19 since version 0 4 20 SC Lovell JM Word JS Richardson and DC Richardson 2000 The Penultimate Rotamer Library Proteins Structure Function and Genetics 40 389 408 You can get the paper from http kinemage biochem duke edu databases rotamer php Chapter 5 Modelling and Building clash flag should the positions of other residues be included in the scoring of the rotamers i e clashing with other other atoms gets marked as bad unlikely lowest rotamer probability some rotamers of some side chains are so unlikely that
250. ouldn t Whenever Coot manipulates the model it saves a backup pdb file There are backup files in the directory coot backup You can recover the session until the last edit by reading in the pdb file that you started with last time and then use File gt Recover Session I would like to know about coot crashing so that I can fix it as soon as possible If you want your problem fixed this involves some work on your part sadly First please make sure that you are using the most recent version of coot I will often need to know as much as possible about what you did to cause the bug If you can reproduce the bug and send me the files that are needed to cause it I can almost certainly fix it especially if you use the debugger gdb and send a backtrace tool Note that you may have to source the contents of bin coot so that the libraries are can be found when the executable dynamically links 8 coot has several influences and dependencies but these will not be discussed here in the User Manual COOT BACKUP DIR is used in preference if set 10 The map reading problem documented in Section Section 6 1 Maps in General page 48 is already known 11 pow there s a hostage to fortune 12 to do so please send me the output of the following gdb which coot real corefile and then at the gdb prompt type where where corefile is the core dump file core or core 4536 or some such Chapter 2 Mousing and Keyb
251. pect an atom selection pick in the graphics window Chapter 5 Modelling and Building To rotate the view when in Delete Mode use Ctrl left mouse If you want to delete multiple items you can use check the Keep Delete Active check button on this dialog This will will keep the dialog open ready for deletion of next item 5 35 Sequence Assignment You can assign a FASTA format sequence to a molecule using assign fasta sequence imol chain id fasta seq This function has been provided as a precursor to functions that will as automatically as possible mutate your current coordinates to one that has the desired sequence It will be used in automatic side chain assignment at some stage in the future 5 36 Building Links and Loops Coot can make an attempt to build missing linking regions or loops This is an area of Coot that needs to be improved currently O does it much better We will have several different loop tools here For now there is Calculate gt Fit Gap or the scripting function fit gap imol chain id start resno stop resno and fit gap imol chain id start resno stop resno sequence the second form will also mutate and try to rotamer fit the provided sequence Example usage let s say for molecule number 0 in chain A we have residues up to 56 and then a gap after which we have residues 62 and beyond fit gap O A 57 61 TYPWS 5 37 Fill Partial Residues After molecular replacement the
252. phere Refinement 60 0 eee cece eee ees 28 5 1 3 Refining Specific Residues 00sec eee cece 29 5 1 4 Refining Carbohydrates 0 cece eee eee eee 29 5 1 5 Planar Peptide Bestrants 0 0 cece eee ee 29 5 1 6 The UNK residue type 20 30 5 1 7 Moving Zero Occupancy Atoms cece eee ee 30 5 2 Changing the Map for Building Refinement 30 bad Rotate Translate Zone dz oe eut adu d cu oh le e 30 5 4 Rigid Body Refinement 0 00 cece eee eee eee eee 30 5 5 Simplex Refinement 2 0 n nee eee 31 5 6 Post manipulation hook sss 31 5 7 Baton Building 4 cede xu be RR RE EQ Re 31 bora Un do rita RLEN NS RES 32 5 7 2 Missing Gkeleton ee 32 5 7 3 Building Backwards 0 00 cece eee eee tees 32 5 8 Reversing Direction of Fragment 0 e eee eee eee 33 5 9 C alpha gt Malnclatmisas d iat yh etre aa 33 5 10 Backbone Torsion Ange 33 5 11 Docking Sidechains 0 00 33 5 12 gt Rotamers it ai LUE CAE 34 BAZ Auto Fit Rotamer 5 c See eee 34 5 12 1 1 Backrub Rotamers 0 0 e eee eee eee eee 35 5 12 2 De clashing residueg 0 00 c cece eee eens 35 5 13 Editing chi Ange 35 5 14 Torsion General 36 5 14 1 Ligand Torsion angles cece cece eee eee 36 ON e EE EE 36 5 16 Add Alternate Conformation 0c cece eee eens 36 Bell MUDA 2 cease bd x A eee ead 37 5 17 1 Mutating DNA RNA dell kept epe ion qus 37 5 17 2 Multiple mutations
253. ple so that the sigma level has been scaled to 1 0 11 43 12 matrix state matrix state function return the relative weight of the geometric terms to the map terms 11 43 13 set refine auto range step set refine auto range step i function Where i is an integer number change the step for autoranging default is 1 Auto ranging alow you to select a range from one button press this allows you to set the number of residues either side of the clicked residue that becomes the selected zone 11 43 14 set refine max residues set refine max residues n function Where n is an integer number set the heuristic fencepost for the maximum number of residues in the refinement regularization residue range Default is 20 Chapter 11 Scripting Functions 11 43 15 refine zone atom index define refine zone atom index define imol ind1 ind2 Where e mol is an integer number e indi is an integer number e ind2 is an integer number refine a zone based on atom indexing 11 43 16 refine zone refine zone imol chain id resnol resno2 altconf Where e imol is an integer number e chain id is a string e resnol is an integer number e resno2 is an integer number e altconf is a string refine a zone presumes that imol_Refinement_Map has been set 11 43 17 refine auto range refine auto range imol chain_id resnol altconf Where e mol is an integer number e chain id is a string e resnol is an integer number e
254. probity radius interactive probe dots molprobity radius function return the radius over which we can run interactive probe 11 94 Map Sharpening Interface 11 94 1 sharpen sharpen imol b factor function Where e imol is an integer number e b factor is a number Sharpen map imol by b factor note of course that positive numbers blur the map Chapter 11 Scripting Functions 11 94 2 set map sharpening scale limit set map sharpening scale limit f Where f is number set the limit of the b factor map sharpening slider default 30 11 95 Marking Fixed Atom Interface 11 95 1 clear all fixed atoms clear all fixed atoms imol Where mol is an integer number clear all fixed atoms 11 96 Partial Charges 11 96 1 show partial charge info show partial charge info imol chain_id resno ins_code Where e imolis an integer number e chain id is a string e resno is an integer number e ins code is a string 173 function function function show the partial charges for the residue of the given specs charges are read from the dictionary 11 97 EM interface 11 97 1 scale cell scale cell mol map fac_u fac_v fac_w Where e mol_map is an integer number e fac_u is a number e fac v is a number e fac w is a number function Scale the cell for use with EM maps where the cell needs to be adjusted Use like scale cell 2 1 012 1 012 1 012 Return error status 1 means it worked 0 means it
255. procedure dialog box of buttons window name geometry buttons procedure close button label a button is a list of label callback thunk text description dialog box of buttons with check button window name procedure geometry buttons close button label check button label check button func check button is initially on flag If check button label is f don t make one otherwise create with with the given label and on state dialog box of pairs of buttons imol window name geometry procedure buttons close button label geometry is an improper list of ints buttons is a list of list list button 1 label button 1 action button 2 label button 2 action The button 1 action function takes as an argument the imol The button 2 action function takes as an argument the imol views panel gui procedure A gui showing views nudge screen centre gui procedure nudge screen centre box Useful when Ctrl left mouse has been taken over by another function make difference map gui procedure A gui to make a difference map from arbitrarily gridded maps that s it s advantage Chapter 13 Scheme Scripting Functions 191 cis peptides gui mol procedure A GUI to display all the CIS peptides and navigate to them associate pir with molecule gui do alignment procedure Associate the contents of a PIR file with a molecule Select file from a GUI alignment mismatches gui imol procedure Make a box of buttons GUI for the various modif
256. r imol Where mol is an integer number change the representation to the next model number to be displayed return 0 on non multimodel molecule 11 108 4 single model view prev model number single model view prev model number mol Where mol is an integer number change the representation to the previous model number to be displayed return 0 on non multimodel molecule function function function function Chapter 11 Scripting Functions 11 109 graphics 2D ligand view 11 109 1 set show graphics ligand view set show graphics ligand view state Where state is an integer number set the graphics ligand view state default is 1 on 11 110 Sectionless functions 11 110 1 get write conect record state get write conect record state return the state of the write_conect_records_flag 11 110 2 set write conect record state set write conect record state state Where state is an integer number set the flag to write or not conect records to the PDB file 11 110 3 make and draw patterson make and draw patterson mtz_file name f_col sigf_col Where e mtz_file name is a string e f_col is a string e sigf_col is a string Make a patterson molecule Returns a new molecule number or 1 on failure 178 function function function function Chapter 12 More Scripting Functions 179 12 More Scripting Functions 12 1 More Symmetry Functions 12 1 1 get symmetry get symmetry im
257. r name for the residue type and a dictionary will be generated for the monomer of this type This function is also a wrapper to LIBCHECK 29 this is a wrapper round LIBCHECK so you must have CCP4 suite to installed for this function to work 30 rather than running LIBCHECK again Chapter 5 Modelling and Building 5 20 Find Ligands You are offered a selection of maps to search you can only choose one at a time and a selection of molecules that act as a mask to this map Finally you must choose which ligand types you are going to search for in this map Only molecules with less than 400 atoms are suggested as potential ligands If you do not have any molecules with less that 400 atoms loaded in Coot you will get the message Error you must have at least one ligand to search for New ligands are placed where the map density is and protein mask atoms are not The masked map is searched for clusters using a default cut off of 1 00 In weak density this cut off may be too high and in such a case the cut off value can be changed using something such as set ligand cluster sigma level 0 8 However if the map to be searched for ligands is a difference map a cluster level of 2 0 or 3 0 would probably be more appropriate less likely to generate spurious sites Each ligand is fitted with rigid body refinement to each potential ligand site in the map and the best one for each site selected and written out as a pdb file The clusters ar
258. raction 0 25 5 unless you are using Buccaneer of course 6 if you want to move only one residue then click the same atom twice 7 like Refinement and Regularization 8 like Regularization and Refinement Chapter 5 Modelling and Building 31 5 5 Simplex Refinement Rigid body refinement via Nelder Mead Simplex minimization is available in Coot Simplex refinement has a larger radius of convergence and thus is useful in a position where simple rigid body refinement finds the wrong minimum However the Simplex algorithm is much slower Simplex refinement for a residue range start resno to end resno inclusive in chain chain id can be accessed as follows fit residue range to map by simplex start resno end resno alt loc chain id imol imol for map There is currently no GUI interface to Simplex refinement 5 6 Post manipulation hook If you wanted automatically run a function after a model has been manipulated then you can do so using by creating a function that takes 2 arguments such as post manipulation hook imol manipulation mode manipulation mode is one of DELETED MUTATED or MOVINGATOMS And of course imol is the model number of the maniplated molecule It would of course be far more useful if this function was also passed a list of residues that is something for the future 5 7 Baton Building Baton build is most useful if a skeleton is already calculated and displayed see Section Section 6 14 Skeletonizatio
259. raints By default Coot uses a 5 atom CA 1 C 1 O 1 N 2 CA 2 planar peptide restraints These restraints should help in low resolution fitting the main chains becomes less distorted reduce accidental cis peptides and may help clean up Ramachandran plots add planar peptide restraints And similarly they can be removed remove planar peptide restraints There is also a GUI to add and remove these restraints in Extensions gt Refine gt Peptide Restraints Chapter 5 Modelling and Building 5 1 6 The UNK residue type The UNK residue type is a special residue type to Coot It has been added for use with Buccaneer Don t give you ligand or anything else the 3 letter code UNK or confusion will result 5 1 7 Moving Zero Occupancy Atoms By default atoms with zero occupancy are moved when refining and regularizing This can sometimes be inconvenient To turn of the movement of atoms with zero occupancy when refining and regularizing set refinement move atoms with zero occupancy 0 5 2 Changing the Map for Building Refinement You can change the map that is used for the fitting and refinement tools using the Select Map button on the Model Fit Refine dialog 5 3 Rotate Translate Zone Rotate Translate Zone from the Model Fit Refine menu allows manual movement of a zone After pressing the Rotate Translate Zone button select two atoms in the graph ics canvas to define a residue range the
260. raphics card and drivers Pass 1 for on 0 for off 11 90 2 display lists for maps state display lists for maps state return the state of display lists for maps 11 91 Browser Interface 11 91 1 browser url browser url url Where url is a string try to open given url in Web browser 11 91 2 set browser interface set browser interface browser Where browser is a string set command to open the web browser examples are open or mozilla function function function Chapter 11 Scripting Functions 168 11 91 3 handle online coot search request handle online coot search request entry_text function Where entry_tezt is a string the search interface find words construct a url and open it 11 92 Generic Objects 11 92 1 new generic object number new generic object number objname function Where objname is a string create a new generic object with name objname and return the index of the object 11 92 2 to generic object add line to generic object add line object_number colour line width from x1 function from_yl Dom zl to_x2 to_y2 to_z2 Where e object number is an integer number e colour is a string e line width is an integer number e from_x1 is a number e from_y1 is a number e from z is a number e io z2 is a number e to_y2 is a number e to_z2 is a number add line to generic object object number 11 92 3 to generic object add dashed line to generic object add dashed line o
261. raw backeround eens 134 11 59 3 backeround As bhackn eee 134 11 60 Ligand Fitting Functions seseseeeeeeeee eee 134 11 60 1 set ligand acceptable fit fraction sssssusususnnnes 134 11 60 2 set beand chuster 2gma Jevel 134 11 60 3 oet beand HBeo ble Deand n sampleg 134 11 60 4 set find ligand n top ligands 0 eee eee eee 134 11 60 5 set find ligand mask waters 0 000 cee eee ee 135 11 60 6 set ligand search protein molecule nususunnn nnana 135 11 60 7 zet beand search map molecule 135 11 60 8 add Deand search beand molecule 135 11 60 9 add ligand search wiggly ligand molecule 135 11 60 10 Deand enert 135 11 60 11 do find ligands dialog nnus esusu unene 135 11 60 12 match Deand atom names 135 11 60 13 flip ligand 0 eee eee es 136 11 61 Water Fitting Functions 0 eee eee eee 136 11 61 1 execute find waters real eee eee 136 11 61 2 move waterg to around protein 0c eee eee 137 11 61 38 move hetgroups to around protein 0005 137 11 61 4 max water distance 0 cece eee eee eee 137 11 61 5 set water check spherical variance limit 137 11 61 6 set ligand water to protein distance limits 137 11 61 7 set ligand water n cycles 6 0 cece eee eee ee eee 137 11 61 8 eecute Dnd bhobe sess 138 11 62 Bond Representation sseeseesee e 138 11 62 1 zet detault bond thickueg
262. re schemey interface to eponymous scripting interface function Return scheme true or false valid refinement map procedure Return t or f shelx molecule imol procedure schemey interface to shelx molecule test Return t or f is difference map imol map procedure Return t or f residue exists imol chain id resno ins code procedure Does residue resno with insertion code ins code of chain chain id and in molecule number imol exist Return t or f residue has hetatms imol chain id res no ins code procedure Does the residue contain hetatoms Return t or f centre of mass imol procedure Return a list of 3 float for the centre of mas of molecule number imol on faiure return f atom specs imol chain id resno ins code atom name alt conf procedure Return as a list the occupancy temperature factor element x y z coordinates of the given atom the x y z are in Cartesian Angstroms on error e g atom not found return f guess refinement map procedure return a guess at the map to be refined usually called after imol refinement map returns 1 target auto weighting value procedure Ian Tickle says as far as I can understand that the target rmsd should be 0 25 or thereabouts You can over ride it now auto weight for refinement procedure Set the refinement weight matrix by iterating the refinement and varying the weight until the chi squares not including the non bonded terms reach 1 0
263. re imol does not have a map 11 17 19 another level another level function Add another contour level for the last added map Currently the map must have been generated from an MTZ file Returns the molecule number of the new molecule or 1 on failure Chapter 11 Scripting Functions 11 17 20 another level from map molecule number another level from map molecule number imap function Where imap is an integer number Add another contour level for the given map Currently the map must have been generated from an MTZ file Returns the molecule number of the new molecule or 1 on failure 11 17 21 residue density fit scale factor residue density fit scale factor function return the scale factor for the Residue Density fit analysis 11 17 22 density at point density at point imol x yz function Where e imol is an integer number e x is a number e y is a number e zis a number return the density at the given point for the given map Return 0 for bad imol 11 18 Parameters from map 11 18 1 mtz hklin for map mtz hklin for map imol map function Where imol map is an integer number return the mtz file that was use to generate the map return 0 when there is no mtz file associated with that map it was generated from a CCP4 map file say 11 18 2 mtz fp for map mtz fp for map imol map function Where mol map is an integer number return the FP column in the file that was use to generate the map return 0 when t
264. re errors imol Where mol is an integer number fix nomenclature errors in molecule number imol Returns the number of resides altered 11 45 2 set nomenclature errors on read set nomenclature errors on read mode Where mode is a string set way nomenclature errors should be handled on reading coordinates 125 function function function function mode should be auto correct ignore prompt The default is prompt Chapter 11 Scripting Functions 126 11 46 Atom Info Interface 11 46 1 output atom info as text output atom info as text imol chain_id resno Ins code atname altconf function Where e mol is an integer number e chain id is a string e resno is an integer number e ins code is a string e atname is a string e altconf is a string output to the terminal the Atom Info for the give atom specs 11 47 Residue Environment Functions 11 47 1 set show environment distances set show environment distances state function Where state is an integer number show environment distances If state is 0 distances are turned off otherwise distances are turned on 11 47 2 set show environment distances bumps set show environment distances bumps state function Where state is an integer number show bumps environment distances lf state is 0 bump distances are turned off otherwise bump distances are turned on 11 47 3 set show environment distances h bonds set show environment distances
265. read the maps the colours of the molecules and map the screen centre map size and so on When restarting a coot session this file should usually be used e O coot history scm The history of coot commands you used in your last coot session in scheme format Incomplete history One day this will be a complete history of the session suitable for uploading into a database describing the model modification e O coot history py The history of coot commands you used in your last coot session in python format e coot download directory where the files downloaded from the network e g from the EBI and EDS go e coot backup Each model modification generates the saving of coordinates as a pdb file in this directory Chapter 9 Hints and Usage Tips 61 e coot refmac When running REFMAC using the Coot interface the input to refmac and the output go in this directory e coot molprobity When running Molprobity s Probe and Reduce using the Coot in terface the input and output go in this directory 9 4 Clearing Backups Coot will occasionally ask you to clear up the coot backup directory You can adjust the behaviour in a number of ways e define clear out backup run n days 3 will run the backup clearance every 3 days the default is every 7 e define clear out backup old days 1 will clear out files older then 1 day rather than the default 7 days e You can create your own version of the function that is run on exiting Coot
266. refix dir 1 existing 2 being a directory 3 modifiable by user ie u rwx Return t or f Chapter 13 Scheme Scripting Functions 198 13 29 mutate from scheme povray version procedure this should negate the need for Bill s patch here povray args procedure args not including the output filename povray image procedure Run provray using current displayed image and write pov file to default filename 13 30 tips tip list procedure a list of tips for Coot no coot tips procedure Function to turn off coot tips at start 13 31 americanisms set rotation center procedure an americanism handle read draw molecule with recenter procedure an americanism set rotation center size procedure an americanism center atom label status procedure an americanism set last map color procedure an americanism center of mass procedure an americanism set swap difference map colors procedure an americanism set font color procedure an americanism set dots color procedure an americanism 13 32 exercise scm mol jiggled mol reference mol current mol traj frac procedure disrupt reference mol biggness procedure Chapter 13 Scheme Scripting Functions 199 13 33 remote control coot listener socket procedure a place holder for the coot listener socket open coot listener socket port number host name procedure Open a coot listener socket return nothing much but do set coot listener socket Hm
267. res in RNADB2005 shows that a critical distance of 3 3A provides a partition function to separate C2 from C3 endo puckering Not all ribose follow this rule There may be some errors in the models comprising RNADB2005 So we check the distance of the following phosphate to the plane of the ribose and record the riboses that are inconsitent We also report puckers that are not C2 or C3 The puckers are determined by the most out of plane atom of the ribose the rms deviation of the 4 atoms in the plane is calculated but not used to determine the puckering atom new molecule by smiles string tlc text smiles text procedure Run libcheck to convert from SMILES string prodrg ify imol chain id res no ins code procedure Generate restraints from the residue at the centre of the screen using PRODRG Delete hydrogens from the residue because PRODRG has anomalous hydrogens add annotation here text procedure save annotations file name procedure load annotations file name procedure make latest version url procedure Here we construct the url that contains the latest pre release info adding in pre release if this binary is a pre release args ends up as something like s xxx phone home scm pre release binary Linux 1386 fedora 10 python gtk2 command line home xx coot bin coot run download binary curl revision version string procedure pending install in place func set file name func Get the binary i e the action t
268. riptions In the future this may simply be the same directory in which refmac looks to find the library dictionary although it does have a local refinement algorithm it is no substitute for refmac a wrapper for refmac is available that s the job of the CCP4 Program Suite so far only 8 2 verified it s Free Software after all and I could give you a hand I can get by with a one button Macintosh but it s not ideal as it is known in Clipper Chapter 1 Introduction 3 COOT_SBASE_DIR The directory to find the SBASE dictionary often comes with CCP4 COOT RESOURCES DIR The directory that contains the splash screen image and the GTK application resources COOT BACKUP DIR The directory to which backup are written if it exists as a directory If it is not then backups are written to the current directory the directory in which coot was started And of course extension language environment variables are used too PYTHONPATH for python modules GUILE LOAD PATH for guile modules Normally these environment variables will be set correctly in the coot shell script 1 6 Command Line Arguments Rather that using the GUI to read in information you can use the following command line arguments c cmd to run a command cmd on start up script filename to run a script on start up but see Section Section 3 10 Scripting page 11 no state script don t run the O coot state scm script on start up Don t save a state s
269. rned on using Info gt Environment Distances Contacts to other residues are shown and to symmetry related atoms if symmetry is being displayed The contacts are coloured by atom typel 4 15 Distances and Angles The distance between atoms can be found using Info gt Distance The result is displayed graphically and written to the console 4 16 Zero Occupancy Marker Atoms of zero occupancy are marked with a grey spot To turn off these markers use set draw zero occ markers 0 Use an argument of 1 to turn them on 4 17 Atomic Dots You can draw dots round arbitrary atom selections dots imol atom selection dot density radius The function returns a handle e g put a sphere of dots around all atoms of the Oth molecule it might be a set of heavy atom coordinates at the default dot density and radius dots 0 1 heavy atom sites 1 1 11 contacts involving two hydrogens or at least one carbon atom are yellow denoting bump Hydrogen contacts display cut off are based on the user defined maximum distance but shortened by 0 5 per hydrogen atom 12 Use Angle for an angle of course Chapter 4 Coordinate Related Features 24 You can t change the colour of the dots There is no internal mechanism to change the radius according to atom type With some cleverness you might be able to call this function several times and change the radius according to the atom selection There is a function to clear up the dots f
270. rom ncs master to others 160 11 81 14 ncs control change ncs master to chain 160 11 81 15 ncs control change ncs master to chain id 160 11 81 16 nes controtdsplav chaim nc 160 11 82 Helices and Strand 160 11 82 1 pGlace heltv here 0 ccc eects 161 11 82 2 place strand here 0 0 e cece eee eee ees 161 11 82 3 pDlace ztrand here dAalog 0 0 cece eee ee eee 161 LR find heli es de ee dE eX 161 11 82 02 Dindsstrands s ma inde AMETS 161 11 82 6 find secondary structure 0 00 eee eee eee eee eee 162 11 82 7 find secondary structure local esses 162 11 83 Nucleotides hentan an ced es its 162 11 83 1 Dnd nucleice acids Jocal eren 162 11 84 New Molecule by Section Interface 163 11 84 1 new molecule by residue type selection 163 11 84 2 new molecule by atom selection oooooooommcocooo o 163 11 84 38 peew molecule b aphere zelection 163 TS ENANA tact eq tte rete taceat o aa teh 163 11 85 1 ideal nucleic acid 0 0 eee eee eens 163 11 85 2 watoon cnckpoair eee eee 164 11 85 38 watson crick pair for residue range ssusss 164 xix 11 86 Sequence Assignment sees 164 11 86 1 print sequence chain o occcooccccconnnccnrrccccn 164 11 86 2 assign fasta sequence 6 cee eee eee ees 165 11 86 83 assign pir sequence oost eee eee 165 11 86 4 assign sequence from file
271. rotein atoms The new waters are optionally created in a new molecule called Waters You have control over several parameters used in the water finding set write peaksearched waters which writes ligand waters peaksearch results pdb which contains the water peaks from the clusters without any filtering and ligand waters pdb which are a disk copy filtered waters that have been either added to the molecule or from which a new molecule has been created set ligand water to protein distance limits min d max d sets the minimum and maximum allowable distances between new waters and the masking molecule usually the protein Defaults are 2 4 and 3 2A set ligand water spherical variance limit varlim sets the upper limit for the density variance around water atoms The default is 0 12 The map that is marked by the protein and is searched to find the waters is written out in CCP4 format as masked for waters map 5 22 1 Refinement Failure Sometimes as a result of water fitting you may see something like WARNING refinement failure start pos xyz 17 1 34 76 60 42 final pos xyz 17 19 34 61 60 59 When Coot finds a blob it does a crude positioning of an atom at the centre of the grid points It then proceeds to move to the peak of the blob by a series of translations There Chapter 5 Modelling and Building 41 are a certain number of cycles and if it doesn t reach convergence by the end of those cycles then you get
272. rovides several graphs that are useful for model validation on a residue by residue basis residue density fit geometry distortion temperature factor variance peptide distor tion and rotamer analysis 7 9 1 Residue Density Fit The density fit graph shows the density fit for residues The score is the average electron density level at the atom centres of the atoms in the residue The height of the blocks is inversely proportional to the density average The residue density fit is by default scaled to a map that is calculated on the absolute scale Sometimes you might be using a map with density levels considerably different to this which makes the residue density fit graph less useful To correct for this you can use the scripting function set residue density fit scale factor factor where factor would be 1 40map as a rule of thumb residue density fit scale factor returns the current scale factor default 1 0 There is also a GUI to this Extensions gt Refine gt Set Density Fit Graph Weight 7 9 2 Rotamer Analysis Residue rotamers are scored according to the prior likelihood Note that when CD1 and CD2 of a PHE residue are exchanged simply a nomenclature error this can lead to large red blocks in the graph apparently due to very unlikely rotamers There are several other residues that can have nomenclature errors like this To fix these problems use fix nomenclature errors imol 7 9 3 Temperature Factor
273. rudimentary file if the coordinates were initially from a PDB file but will contain substantial SHELX commands if the coordinates were initially generated from a SHELX ins file 4 2 Atom Info Information about about a particular atom is displayed in the text console when you click using middle mouse Information for all the atoms in a residue is available using Info gt Residue Info The temperature factors and occupancy of the atoms in a residue can be set by using Edit gt Residue Info 4 3 Atom Labeling Use Shift left mouse to label atom Do the same to toggle off the label The font size is changeable using Edit gt Font Size The newly centred atom is labelled by default To turn this off use set label on recentre flag 0 Some people prefer to have atom labels that are shorter without the slashes and residue name set brief atom labels 1 To change the atom label colour use set font colour 0 9 0 9 0 9 4 4 Atom Colouring The atom colouring system in coot is unsophisticated Typically atoms are coloured by element carbons are yellow oxygens red nitrogens blue hydrogens white and everything else green see Section Section 3 7 Display Manager page 10 for colour by chain However it is useful to be able to distinguish different molecules by colour so by default coot rotates the colour map of the atoms i e changes the H value in the HSV colour system The amount of the rotation depends
274. s 11 8 1 set do anti aliasing set do anti aliasing state Where state is an integer number set the bond lines to be antialiased 11 8 2 do anti aliasing state do anti aliasing state return the flag for antialiasing the bond lines 11 8 3 set do GL lighting set do GL lighting state Where state is an integer number turn the GL lighting on state 1 or off state 0 slows down the display of simple lines 11 8 4 do GL lighting state do GL lighting state return the flag for GL lighting 11 8 5 use graphics interface state use graphics interface state shall we start up the Gtk and the graphics window function function function function function if passed the command line argument no graphics coot will not start up gtk itself An interface function for Ralf 11 8 6 start graphics interface start graphics interface start Gtk and graphics function This function is useful if it was not started already which can be achieved by using the command line argument no graphics An interface for Ralf 11 8 7 reset view reset view Reset the view return 1 if we moved else return 0 function centre on last read molecule with zoom 100 If we are there then go to the previous molecule if we are there then go to the origin Chapter 11 Scripting Functions 11 8 8 graphics n molecules graphics n molecules function return the number of molecules coordinates molecules
275. s 00 eee e eee 129 11 54 1 do ramachandran plot 2 0 0 cece eee eee 129 11 54 2 zet klevwegt plot n dffs 0 00 eee eee eee 129 11 54 38 set ramachandran plot contour levels 130 11 54 4 set ramachandran plot background block size 130 11 54 5 ramachandran plot dfferences ccc ee ee 130 11 54 6 ramachandran plot differences by chain 130 11 55 Sequence View Interface 130 11 55 1 do sequence view 0 cece cece een ees 130 11 56 Atom Labelling mi A EEN 131 11 56 1 set brief atom labels oooooooocococooonnnnorooooo 131 11 56 2 brief atom labels state ooooooooccococnonocoonooooo 131 11 57 Screen Rotation sese RR 131 11 57 1 rotate y scene 2 eee eee eee ee 131 11 57 2 rotatevacene eee cece Ie 131 11 57 3 rotate z scene 6 eee eee ne 131 11 57 4 spin zoom trans 0 eee ee eee 131 11 58 Views Interface 132 11 58 1 add view here cece cee cece ees 132 11 58 2 add view raw dti oaa EEE E e eens 132 11 58 38 remove named view 0 00 e cece eee ees 132 11 58 4 rermove view 132 11 58 5 add view description cc 133 11 58 6 add action view 0 0 cece eee eee 133 11 58 7 insert action view after view 0 00 c eee eee eee 133 11 58 8 SAVESVIEWS sss ote Aiea bev a eset 133 11 58 9 clear alviews 0 cece cee cee eee nees 133 11 59 Background Cola 133 11 59 1 set backeround colour sees 134 11 59 2 red
276. s an integer number e offset is an integer number renumber the given residue range by offset residues 11 40 2 change residue number change residue number imol chain_id current resno current inscode function new resno new inscode Where e imolis an integer number e chain id is a string e current resno is an integer number e current inscode is a string e neu resno is an integer number e neu inscode is a string change chain id residue number or insertion code for given residue 11 41 Scripting Interface 11 41 1 probe available p probe available p function Can we run probe was the executable variable set properly predicate Returns 1 for yes 2 for no Chapter 11 Scripting Functions 118 11 41 2 post scripting window ost scripting window function p pting do nothing compatibility function 11 41 3 post scheme scripting window post scheme scripting window function pop up a scripting window for scheming 11 41 4 post python scripting window post python scripting window function pop up a scripting window for pythoning 11 42 Monomer 11 42 1 get coords for accession code get coords for accession code code function Where code is a string if possible read in the new coords getting coords via web no return value because get url str does not return one 11 42 2 get monomer get monomer three_letter_code function Where three_letter_code is a string import libcheck monomer give the 3
277. s for molecule number imol 11 81 2 draw ncs ghosts state draw ncs ghosts state imol function Where mol is an integer number return the drawing state of NCS ghosts for molecule number imol Return 1 on imol is a bad molecule or no ghosts 11 81 3 set ncs ghost bond thickness set ncs ghost bond thickness imolf function Where e imol is an integer number e fisa number set bond thickness of NCS ghosts for molecule number imol 11 81 4 ncs update ghosts ncs update ghosts imol function Where mol is an integer number update ghosts for molecule number imol 11 81 5 make dynamically transformed ncs maps make dynamically transformed ncs maps imol model imol map function overwrite maps of same name flag Where e mol model is an integer number e imol map is an integer number Chapter 11 Scripting Functions e overwrite_maps_of_same_name _flag is an integer number make NCS map 11 81 6 add ncs matrix add ncs matrix imol this chain id target_chain_id m11 m12 m13 m21 m22 m23 m31 m32 m33 t1 t2 t3 Where imol is an integer number this_chain_id is a string target_chain_id is a string mi is a number m12 is a number m13 is a number m21 is a number m22 is a number m23 is a number m31 is a number m3 2 is a number m33 is a number t1 is a number 12 is a number 13 is a number Add NCS matrix 11 81 7 add strict ncs matrix add strict ncs matrix imol this chain id target chain id m11 m12 m13 m2
278. s gui window name sorting options cluster list procedure list cluster name string cluster center go button label string ccgb x ccgb y ccgb z now a list of specific items list list specific button label string button red button green button blue specific x specific y specific z list specific button label string button red button green button blue specific x specific y specific z 13 21 libcheck libcheck exe procedure this is override able by the user in their coot file for example monomer molecule from 3 let code code dict cif libin procedure ccp4i project dir Return 2 on code is not a string Return 3 on libcheck failure Return imol on success Return handle read draw molecule error code on failure to read resultant pdb file Chapter 13 Scheme Scripting Functions 194 Actually it would be nice to know if this code represented a full description or a minimal one perhaps we can parse the log file and call a pop up that will tell us dict cif libin should be a string If it is then it is ignored If it is not then it is used to create input to libcheck not a command line argument so that bespoke dictionary libraries can produce coords using Get Monomer 13 22 generic objects generic object is displayed procedure map to scheme names is closed generic object procedure map to scheme names generic object with name procedure return a new generic object number for the given object obj name If t
279. s of a ligand using this tool you will need to have read in the mmCIF dictionary beforehand 5 14 Torsion General You need to click on the torsion general button then click 4 atoms that describe the torsion the first atom will be the base non moving part of the atom tree on clicking the 4th atom a dialog will pop up with a Reverse button Move this dialog out of the way and then left mouse click and drag in the main window will rotate the top part of the residue round the clicked atoms 2 and 3 When you are happy click Accept If you are torsion generaling a residue that has an alt conf then the atoms of residue that are moved are those that have the same alt conf as the 4th clicked atom or have an blank alt conf 5 14 1 Ligand Torsion angles For ligands you will need to read the mmCIF file that contains a description of the ligand s geometry see Section Section 5 1 Regularization and Real Space Refinement page 27 By default torsions that move hydrogens are not included Only 9 torsion angles are available from the keyboard torsion angle selection 5 15 Pep flip Coot uses the same pepflip scheme as is used in O i e the C N and O atoms are rotated 180 round a line joining the Co atoms of the residues involved in the peptide Flip the peptide again to return the atoms to their previous position 5 16 Add Alternate Conformation The allows the addition alternate dual triple etc conformations to the picked r
280. s of buttons 190 dictionaries read sss 180 difference map eee eee eee 87 difference map peaks esses 129 directory as file name 204 directory files p i isk cms 204 211 212 directory is modifiable 197 201 display lists for maps state 167 disrupt isn sie A eibi dee n reme ei 198 do 180 degree side chain flip 149 do anti aliasing starte sss 72 do find ligands dialog 135 do Gl Ligbting atate sss 72 do probe dots on rotamers and chis state SE 172 do probe dots post refine state 172 do ramachandran plot sssss 129 do Seduence vley co 130 dossmiles gui ose enr pnie ias toga 174 ek te EE 166 does Cesidue eriet p 123 dOtS SEENEN EERSTEN EE EEN 142 download binary dialog sssssssssse 197 drag intermediate atom 185 dragged refinement steps per frame 122 d raw hudrogene State sssr 139 draw ncs ghosts etate ro 157 E edit chi anglesg 6 cece eee eee ee 153 esoteric depth cue state 0 92 Function Index eval socket string lesse 199 e EE 204 exchange chain ids for seg ids 70 execute find blobs o oo o ooooooomoooo 138 execute find waters real 136 execute refmac real 0 cece ee eee 179 export map e jecit suu ad Lata Shand ok 86 export map fragment
281. scribed in the manual simple 1sq match ref start resno ref end resno ref chain id imol ref procedure mov start resno mov end resno mov chain id imol mov match type Simple interface to LSQ fitting More often than not this is what you will want I imagine e g simple Isq match 940 950 A 0 940 950 A 1 main Concept Index Concept Index alternate conformation s eressrrrerers 36 anisotropic atoms eene 22 annotbablons scenes a MEUM EE 17 atom Colouring 6 UIS UO 10 19 AOI JB O ian uestes Leer ST Pes ER pd 19 atom label beet A eI 19 atom labeling 2i pepe t RH 19 atom picking 0 cece eee eee eee eee 44 atomic dOtS compi diia p Gl RI eve lees 23 auto fit rotamer sees ire 0 cece eee eee 34 Average MAD EE 51 B B Factor New Atoms sees 42 background color 16 backrub rotamerg 0 00 e cece eee 35 Daeki ps acc a aaa 13 backups clearing sscssecueurerreeseeeene 61 ball and stick eascair ateoa a Weak eens 24 baton buds iman rre n u ini iee 31 baton Mode resi A EE AE EEE 31 big MAPS A EA eee 51 Dlobe 24 E ed eh A 56 bond thickness 20 bones i m 9 x RR Gui dre iy xliv 52 C Csterminig 2 2 ie tine el pelrt u lehesemitena 41 C alpha representation sese cee eee eee 10 C alpha symmetry see 22 carbohydrates n cocszeonpibrrseserv ines 29 Chain 1d iso tile DRIN es 45 change contour level ssusnusrrrrrnrrrue 48 changing chain idee 45 changing
282. se the option menu to choose the map and click On then OK to the generate the map the skeleton is off by default The level of the skeleton can be changed by using Edit gt Skeleton Parameters gt Skeletonization Level and corresponds to the electron density level in the map By default this value is 1 2 map standard deviations The amount of map can be changed using Edit gt Skeleton Parameters gt Skeleton Box Radius The units are in Angstr ms with 40 as the default value The skeleton is often recalculated as the screen centre changes but not always since it can be an irritatingly slow calculation If you want to force a regeneration of the displayed skeleton simply centre on an atom using the middle mouse button or press the S key 6 15 Map Sharpening It can be educational even useful at lower resolutions to sharpen or blur a map This can be achieved with the sharpening tool Calculate gt Map Sharpening By default the maximum and minimum sharpness is 304 this can be changed in this case to 80 using set map sharpening scale limit 80 This currently only works on maps created by reading an MTZ or other reflection data file 6 16 Pattersons Pattersons can be generated using the make and draw patterson function Example us age make and draw patterson mtz file name f col sig f col weight col use weights flag where use weights flag is either O or 1 6 17 Masks A map can be
283. sequence is a string create a molecule of idea nucleotides use the given sequence single letter code DNA or DNA is either RNA or DNA form is either A or B Returns the new molecule number or 1 if a problem 11 85 2 watson crick pair watson crick pair mol chain jd resno function Where e imol is an integer number e chain_id is a string e resno is an integer number Return a molecule that contains a residue that is the WC pair partner of the clicked picked selected residue 11 85 3 watson crick pair for residue range watson crick pair for residue range imol chain id resno start function resno_end Where e mol is an integer number e chain id is a string e resno_start is an integer number e resno_end is an integer number add base pairs for the given residue range modify molecule imol by creating a new chain 11 86 Sequence Assignment 11 86 1 print sequence chain print sequence chain imol chain id function Where e imol is an integer number e chain d is a string Print the sequence to the console of the given molecule Chapter 11 Scripting Functions 11 86 2 assign fasta sequence assign fasta sequence imol chain_id_in seq Where e mol is an integer number e chain_id_in is a string e seq is a string Assign a FASTA sequence to a given chain in the molecule 11 86 3 assign pir sequence assign pir sequence imol chain Ad Im seq Where e imolis an integer number e chain id in
284. set show symmetry molecule 2 0c eee eee 96 11 21 5 owmmetre as calpnhas 0 cece eee eee 96 11 21 6 get symmetry as calphas state 0 0 cece eee eee 96 11 21 7 set symmetry molecule rotate colour map 97 11 21 8 symmetry molecule rotate colour map state 97 11 21 89 has unit cell state 0 0 eee cee ee 97 11 21 10 umndo swvmmetrv ieug cece eee eh 97 11 21 11 first molecule with symmetry displayed 97 11 21 12 save symmetry coords esses eese 97 11 21 13 new molecule bn aummetrw 00 cee eee eee eee 98 11 21 14 new molecule by symmetry with atom selection 98 11 21 15 new molecule by symop 0 2 eee e eee eee eens 99 l1L21 16 mnssymopS o is Bete tat ee Mie ee 99 11 21 17 set space grouP 1 i cece e 100 11 21 18 set symmetry shift search SiZO ooooocccoomomo 100 11 22 History BunctiO0nS cde ky RIS ai EEN 100 11 22 1 print all history in scheme ssesssseeesesse 100 11 22 2 print all history in python 00 eee eee eee 100 11 22 38 set console display commands state susussssus 100 11 22 4 set console display commands hilights 100 11 23 State Functions iesene ce mus Ee Cp VOR 101 14 292 EE 101 11 23 2 save state file 0 0 cee eens 101 11 23 3 set save state file name 0 cece eee eee eee 101 11 23 4 set run state file status sse 101 11 28 5 ron statehle rca 101 11 23 6 run
285. shift 43 R W W Hooft G Vriend C Sander E E Abola Errors in protein structures Nature 1996 381 272 272 Chapter 5 Modelling and Building will translate all the atoms in molecule imo1 by the given amount in Angstr ms move molecule to screen centre imol will move the imolth molecule to the current centre of the screen sometimes useful for imported ligands Note that this moves the atoms of the molecule not just the view of the molecule 5 44 Modifying the Labels on the Model Fit Refine dialog If you don t like the labels Rotate Translate Zone or Place Atom at Pointer and rather they said something else you can change the button names using set model fit refine rotate translate zone label Move Zone and set model fit refine place atom at pointer Add Atom Chapter 6 Map Related Features 6 Map Related Features 6 1 Maps in General Maps are infinite not limited to pre calculated volume the Everywhere You Click There Is Electron Density EYC TIED paradigm symmetry related electron density is generated automatically Maps are easily re contoured Simply use the scroll wheel on you mouse to alter the contour level or on the keyboard Maps follow the molecule As you recentre or move about the crystal the map quickly follows If your computer is not up to re contouring all the maps for every frame then use Draw gt Dragged Map to turn off this feature 6 1 1 Map R
286. state Dle mavbe 0 0 cece eee ee eee 101 11 24 Unit Cell interface aaa 102 11 24 1 get abhow mmt cell ere sese ee 102 11 24 2 set show unit cells all 0 0 0 een ee 102 11 24 3 set show unit cell 0 0c eee eee 102 TL25 EE 102 11 25 1 set colour map rotation on read pdb ssss 102 11 25 2 set colour map rotation on read pdb flag 102 11 25 38 set colour map rotation on read pdb c only flag 102 11 25 4 zet colour bv chaim eee eee ee 102 11 25 5 set colour by molecule 0 00 c cece eee eee eee 103 11 25 6 set symmetry colour 0 0 e eee eee 103 11 26 Map colours erepto eR er reto tai 103 11 26 1 set colour map rotation for Map sssssesesessesss 103 11 26 2 set molecule bonds colour map rotation 103 11 26 3 get molecule bonds colour map rotation 103 11 27 Display Punctions tdci eben DE Tee EEs 103 11 27 1 set graphics window size 0 cece eee eee 104 11 27 2 set graphics window position 00 e eee eee 104 11 27 39 graphics draw oed e ela Rte VL yee 104 11 27 4 zalman stereo m0ode cece cece eee eee eee eee 104 11 27 5 bardeare stereo mode 0 0 e eee eee eee eee 104 11 27 6 otereo mode state 0 0 ccc eee eee eee 104 TL 20 MoOno Modess 5 me ko ea ee a aAa A 104 11 27 8 side by side stereo mode 000 e cece e eee eee 104 11 27 9 zet hardware ztereo angle fIoctor 105 11 27 10 hardware stereo a
287. state of the above option 11 43 23 set refine ramachandran angles set refine ramachandran angles state function Where state is an integer number turn on Ramachandran angles refinement in refinement and regularization 11 43 24 set fix chiral volumes before refinement set fix chiral volumes before refinement istate function Where istate is an integer number correct the sign of chiral volumes before commencing refinement Do we want to fix chiral volumes by moving the chiral atom to the other side of the chiral plane if necessary Default yes 1 Note doesn t work currently 11 43 25 check chiral volumes check chiral volumes imol function Where mol is an integer number query the state of the above option Chapter 11 Scripting Functions 123 11 43 26 set show chiral volume errors dialog set show chiral volume errors dialog istate function Where istate is an integer number For experienced Cooters who don t like Coot nannying about chiral volumes during refinement 11 43 27 set secondary structure restraints type set secondary structure restraints type itype function Where itype is an integer number set the type of secondary structure restraints 0 no sec str restraints 1 alpha helix restraints 2 beta strand restraints 11 43 28 secondary structure restraints type secondary structure restraints type function return the secondary structure restraints type 11 43 29 imol refinement map imol refineme
288. step such steps 11 57 2 rotate x scene rotate x scene nsteps stepsize Where e nsteps is an integer number e stepsize is a number rotate view round x axis stepsize degrees for nstep such steps 11 57 3 rotate z scene rotate z scene nsteps stepsize Where e nsteps is an integer number e stepsize is a number rotate view round z axis stepsize degrees for nstep such steps 11 57 4 spin zoom trans Spin zoom trans axis nstep stepsize zoom by x rel y rel z rel Where e axis is an integer number 131 function function function function function function Chapter 11 Scripting Functions 132 e nstep is an integer number e stepsize is a number e zoom_by is a number e z_rel is a number e y rel is a number e z rel is a number Bells and whistles rotation spin zoom and translate where axis is either x y or z stepsize is in degrees zoom by and x rel etc are how much zoom x y z should have changed by after nstep steps 11 58 Views Interface 11 58 1 add view here add view here view_name function Where view_name is a string return the view number 11 58 2 add view raw add view raw rcx rcy rcz quat1 quat2 quat3 quat4 zoom view name function Where e rcr is a number e rcy is a number e rcz is a number e quati is a number e quat2 is a number e quat is a number e quat4 is a number e zoom is a number e view name is a string return the view number 11 58 3 remove na
289. t e g list list 100 010001 list 4 5 0 4 1 2 transform map procedure transform map imol mat trans about pt radius space group cell where space group is a HM symbol and cell is a list of 6 parameters where the cell angles are in degrees or transform map imol trans about pt radius for a simple translation or transform map imol trans radius when using the default rotation centre as the about pt get first ncs master chain procedure return then NCS master of the first molecule that has ncs return on fail to find an ncs chain transform map using lsq matrix imol ref ref chain ref resno start procedure ref resno end imol mov mov chain mov resno start mov resno end imol map about pt radius Remember that now the about pt is the to point i e the maps are brought from somewhere else and generated about the about pt brighten map imol scale factor procedure Make the imol th map brighter brighten maps procedure Make all maps brighter darken maps procedure Make all maps darker chain ids imol procedure Return a list of chain ids for given molecule number imol return empty list on error is solvent chain imol chain id procedure convert from interface name to schemish name Return t or f valid model molecule imol procedure schemey interface to eponymous scripting interface function Return scheme true or false Chapter 13 Scheme Scripting Functions 207 valid map molecule imol procedu
290. t all history in scheme 100 print header secondary structure info 69 Drint mnolecule names esee 209 print seg entes ebrea oe haa up ve 207 Drint Seguence chain 164 PLINt ViSw MAC a o 77 Probeer means inenen io 194 probe available p cece eee eee 117 probe local sphere cece eee 194 problem residues gt dialog 192 prodrg flat x4c0e1i2 Rae ie ete a 193 prodre Ify A eka eee ee hela te 210 prodrg xyzin it hee SA 193 protein db loops eee 183 p kka cpuckers 5 8 RE Me AA 210 Q QUICK ES AV O ais Wess A 94 R ramachandran plot differences 130 ramachandran plot differences by chain 130 TAMBO tas ts dd IIS B 202 rapper dir tai sa es 186 197 raster screen shot ccccoccccccccccccco 155 rastergd miii a 154 E EE 197 223 readspadbcallb c ofer ol EE 204 read phs and coords and make map 111 read phs and make map using cell symm 111 read phs and make map using cell symm from MOA 8 gt ew E NAO 111 read phs and make map using cell symm from Drevious nol i a Ai 111 read phs and make map with reso limits 112 read shelx ins file lusus 128 read shelx 1lstrfile oocoooomooo 192 read vu file oua ie eb ne 208 reattach modelling toolbar 79 recover sesSion ls do oeit Sane ENN 83 redraw background cece eee eeee 134 reduce on pdb file
291. t map radius set map radius f function Where f is number set the extent of the box radius of electron density contours 11 17 12 set density size set density size f function Where f is number another old way of setting the radius of the map Chapter 11 Scripting Functions 11 17 13 set display intro string set display intro string str function Where str is a string Give me this nice message str when I start coot 11 17 14 get map radius get map radius function return the extent of the box radius of electron density contours 11 17 15 set esoteric depth cue set esoteric depth cue istate function Where istate is an integer number not everone likes coot s esoteric depth cueing system Pass an argument istate 1 to turn it off this function is currently disabled 11 17 16 esoteric depth cue state esoteric depth cue state function native depth cueing system return the state of the esoteric depth cueing flag 11 17 17 set swap difference map colours set swap difference map colours i function Where i is an integer number not everone lies coot s default difference map colouring Pass an argument i 1 to swap the difference map colouring so that red is positve and green is negative 11 17 18 set map is difference map set map is difference map imol function Where mol is an integer number post hoc set the map of molecule number imol to be a difference map Returns success status 0 failu
292. t provide good results 2 to anneal the newly added residue back to the clicked residue no matter where it ended up being positioned set add terminal residue do post refine 1 3 set add terminal residue n phi psi trials 200 will change the number of tri als default is 100 This is useful if you think that Coot needs to search harder to find a good solution to the positioning of the next residue 5 24 Add OXT Atom to Residue At the C terminus of a chain of amino acid residues there is a modification so that the C O becomes a carbonyl i e an extra terminal oxygen OXT needs to be added This atom is added so that it is in the plane of the Co C and O atoms of the residue Scripting usage add OXT to residue imol residue number insertion code chain id where insertion code is typically Note in order to place OXT the N CA C and O atoms must be present in the residue if for example the existing carbonyl oxygen atom is called OE1 then this function will not work 32 usually if this still fails after two repetitions then it never seems to work 33 The map is selected using Refine Regularize Control uic e g add OXT to residue 0 428 A Chapter 5 Modelling and Building 5 25 Add Atom at Pointer By default Add Atom At Pointer will pop up a dialog from which you can choose the atom type you wish to insert Using set pointer atom is dummy 1 you can by pass this dialog and immediately cr
293. ta buie e eet ea ete 11 3 9 1 File name Filtering 0 cece eee eee eee 11 3 9 2 Filename Sorting 0 cece eee eee 11 3 9 3 Save Coordinates Director 11 SAO CEBI rege ENEE E 11 2 10 1 Python iro ee ee ed 12 3 10 1 1 Python Commande 12 3 10 2 SCHEME so kt teur rire a s hu ees d EE E 12 3 10 3 Coot State i i iie des 12 3210 4 Key Bindings ad tetas mati 13 3 10 5 User Defined Functions 0 000 e cece eee eee 13 3 11 Backups and Undo sess e m eee aaa 13 SIEM Redonda EE a 14 3 11 2 Restoring from Backup 14 3427 Vie W Matrix acidic fete ta ia seen ones cath ah han RR 14 3 13 Space Group and Symmetry 0 cece eee eee 15 3 14 Recentring Vie Wii Se ae Pea ERO Hee 15 SM MAIS e E ee ee ee Ree 15 3 16 Clipping Manipulation ssseseeeeeeee 16 3 17 Background color 16 948 Unit Cellizzc teni cn tases eM RW E ES e Rea 16 3 19 Rotation Centre Pointer 0 00 cece cence een ees 16 3 20 Orientation Axe 16 3 21 Pointer Distances ioco ule eb EUER UPS REIR Fd e 16 3 22 Crosshairs ducas e nee te RR RR UPC e A 16 329 E Annotations ccnperterevereeiexmfe We Meena re S 17 3 24 Frame Rotura rra ls oe pese hel 17 3 25 Program Output s 242544 ceed a A EN E LER QUU IE 17 Coordinate Related Features 18 4 1 Reading coordinates en 18 4 1 1 A Note on Space Groups Names sssuusersnrsues 18 4 1 2 Read multiple coordinate Des 18 4 1 3 SHELX ins res TOS acia be RE RU rat 18
294. ter 4 Coordinate Related Features 21 4 5 4 NCS Maps Coot can use the relative transformations of the NCS related molecules in a coordinates molecule to transform maps Use Calculate gt NCS Maps to do this note the NCS maps only make sense in the region of the reference chain see above Note also that the internal representation of the map is not transformed If you try to export a NCS overlay map you will get an untransformed map A transformed map only makes sense around a given point and when using transformed maps in Coot this reference point is changed on the fly thus allowing map transformations on the fly This applies to NCS overlap maps NCS averaged maps are transformed This will also create an NCS averaged map 4 5 5 Using Strict NCS Coot can use a set of strict NCS matrices to specify NCS which means that NCS related molecules can appear like convention symmetry related molecules add strict ncs matrix imol ncs chain id ncs target chain id m11 m12 m13 m21 m22 m23 m31 m32 m33 t1 t2 t3 where ncs chain id might be B C D etc and ncs target chain id is A i e the B C D molecules are NCS copies of the A chain for icosahedral symmetry the translation components t1 t2 t3 will be 0 You need to turn on symmetry for molecule imol and set the displayed symmetry object type to Display Near Chains 4 6 Download coordinates Coot provides the possibility to download coordinates from an OCA e g
295. the error message Often when you go to the position indicated you can see why Coot had a problem in the refinement 5 22 2 Blobs After a water search Coot will create a blobs dialog see Section Section 7 4 sec_blobs page 56 5 23 Add Terminal Residue This creates a new residue at the C or N terminal extension of the residue clicked by fitting to the map du angle pairs are selected at random based on the Ramachandran plot probability for a generic residue and fitted to the density By default there are 100 trials It is possible that a wrong position will be selected for the terminal residue and if so you can reject this fit and try again with Fit Terminal Residue Each of the trial positions are scored according to their fit to the map and the best one selected It is probably a good idea to run Refine Zone on these new residues If you use the Extensions Dock Sequence gt Associate Sequence with Model to apply a PIR sequence file to a model then Add Terminal Residue will use the sequence alignment to determine the residue type of the added residue Sometimes particularly with low resolution maps the added terminal residue will wander off to somewhere inappropriate This can be addressed in a number of ways 1 set terminal residue do rigid body refine 0 will disable rigid body fitting of the terminal residue fragment for each trial residue position the default is 1 on this may help if the search does no
296. the molecule i e move the coordinates of some of atoms the Ramachandran plot gets updated to reflect those changes Also the underlying 1 probability density changes according to the selected residue type i e the residue under the mouse in the plot There are 3 different residue types GLY PRO and not GLY or PRO When you mouse over a representation of a residue a little square or triangle the residue label pops up The residue is active 2 e it can be clicked The graphics view changes so that the Co of the selected residue is centred In the Ramachandran plot window the current residue is highlighted by a green square The underlying distributions are taken from the Richardson s Top500 structures http kinemage biochem duke edu databases top500 php The probability levels for acceptable yellow and preferred red are 0 2 and 2 re spectively You can change the contour levels set ramachandran plot contour levels 0 025 0 003 You can change the blocksize the default is 10 degrees of the contours using set ramachandran plot background block size 5 These comes into effect when a new plot is created it doesn t change plots currently displayed 7 2 Geometry Analysis A restraints based geometry analysis of the molecule The distortion is weighted by atom occupancy The distortion of the geometry due to links is shared between the contributing residues Note that only the first model of a multi m
297. tion Where e isa number e jisa number e k is a number e lisa number Set the view quaternion 11 9 8 apply ncs to view orientation apply ncs to view orientation imol current chain next ncs chain function Where e imolis an integer number e current chain is a string e mert ges chan is a string Given that we are in chain current chain apply the NCS operator that maps cur rent chain on to next ncs chain so that the relative view is preserved For NCS skipping 11 9 9 apply ncs to view orientation and screen centre apply ncs to view orientation and screen centre imol function current chain next_ncs_chain forward flag Where e imolis an integer number e current chain is a string e mert ges chan is a string forward flag is an integer number as above but shift the screen centre also 11 9 10 set show origin marker set show origin marker istate function Where istate is an integer number set a flag is the origin marker to be shown 1 for yes 0 for no Chapter 11 Scripting Functions 11 9 11 show origin marker state show origin marker state function return the origin marker shown state 11 9 12 hide modelling toolbar hide modelling toolbar function hide the vertical modelling toolbar in the GT K2 version 11 9 13 show modelling toolbar show modelling toolbar function show the vertical modelling toolbar in the GTK2 version the toolbar is shown by default 11 9 14 hide main to
298. tly Use for example set matrix 20 0 to change the weight of the map gradients to geometric gradients The higher the number the more weight that is given to the map terms The default is 60 0 This will be needed for maps generated from data not on or close to the absolute scale or maps that have been scaled for example so that the sigma level has been scaled to 1 0 For both Regularize Zone and Refine Zone one is able to use a single click to refine a residue range Pressing A on the keyboard while selecting an atom in a residue will automatically create a residue range with that residue in the middle By default the zone is extended one residue either size of the central residue This can be changed to 2 either side using set refine auto range step 2 Intermediate white atoms can be moved around with the mouse click and drag with left mouse by default Refinement will proceed from the new atom positions when the mouse button is released It is possible to create incorrect atom nomenclature and or chiral 1 given a half decent window manager 2 Diamond R 1971 A Real Space Refinement Procedure for Proteins Acta Crystallographica A27 436 452 3 but the resulting x values are higher Chapter 5 Modelling and Building 28 volumes in this manner so some care must be taken Press the A key as you left mouse click to move atoms more locally rather than a linear shear and CTRL key as you left mouse click to
299. tly created file procedure return f on no such file Chapter 13 Scheme Scripting Functions residue spec gt atom selection string centre residue spec Convert a residue spec to an mmdb atom selection string residue atom gt atom name ra residue info atom residue atom gt alt conf ra residue info atom residue spec gt chain id rs residue spec e g from residue near residue map molecule list Return a list of molecules that are maps model molecule list Return a list of molecules that are maps shelx molecule imol Return t f if imol is isn t a shelx molecule set virtual trackball type type Set the virtual trackball behaviour trackball type is a symbol either flat or spherical surface list of strings ls Is Is a list of strings Return t or f coot replace string string in target replacing str coot replace string one two three gt one two three string append with spaces ls string concat with spaces Is must be a list of strings rotation centre The screen centre return the rotation centre as a 3 membered list of numbers number list ab Make list of integers a to b eg number list 2 5 gt 2 3 4 5 string member atom ls ls must be a list of strings atom must be a string return either t or f member atom ls range first second range works like the eponymous python function e g range 3 gt range 1 3 gt 1 2 202 procedure procedure pro
300. ton shorten baton function shorten the baton length 11 73 6 lengthen baton lengthen baton function lengthen the baton 11 73 7 baton build delete last residue baton build delete last residue function delete the most recently build CA position 11 73 8 set baton build params set baton build params istart resno chain_id direction function Where e istart_resno is an integer number e chain id is a string e direction is a string set the parameters for the start of a new baton built fragment direction can either be forwards or backwards 11 74 Crosshairs Interface 11 74 1 set draw crosshairs set draw crosshairs i function Where i is an integer number draw the distance crosshairs 0 for off 1 for on 11 75 Edit Chi Angles Chapter 11 Scripting Functions 153 11 75 1 set find hydrogen torsions set find hydrogen torsions state function Where state is an integer number show torsions that rotate hydrogens in the torsion angle manipulation dialog Note that this may be needed if in the dictionary cif file torsion which have as a 4th atom both a hydrogen and a heavier atom bonding to the 3rd atom but list the 4th atom as a hydrogen not a heavier atom 11 75 2 edit chi angles edit chi angles imol chain_id resno ins_code altconf function Where e mol is an integer number e chain id is a string e resno is an integer number e ins code is a string e altconf is a string display the edit c
301. try imol name m11 m12 m13 m21 m22 m23 function m81 m32 m33 tx ty tz pre_shift_to_origin_na pre_shift_to_origin_nb pre_shift_to_origin_nc Where e mol is an integer number e name is a string e m11 is a number e m12 is a number e m13 is a number e m1 is a number e m22 is a number e m23 is a number e m31 is a number e m32 is a number e m33 is a number e tx is a number e ty is a number e tz is a number e pre_shift_to_origin_na is an integer number e pre_shift_to_origin_nb is an integer number e pre_shift_to_origin_nc is an integer number create a new molecule molecule number is the return value from imol The rotation translation matrix components are given in orthogonal coordinates Allow a shift of the coordinates to the origin before symmetry expansion is aplied Pass as the name in and a name will be constructed for you Return 1 on failure 11 21 14 new molecule by symmetry with atom selection new molecule by symmetry with atom selection imol name function mmdb atom selection string m11 m12 m13 m21 m22 m23 m31 m32 m33 tx ty tz pre_shift_to_origin_na pre_shift_to_origin_nb pre_shift_to_origin_nc Where Chapter 11 Scripting Functions e mol is an integer number e name is a string e mmdb_atom_selection_string is a string e mii is a number e m12 is a number e m13 is a number e m21 is a number e m22 is a number e m23 is a number e m31 is a number e m32 is a number e m33 is a number
302. tter if it has a scroll wheel too see Chapter 2 for more details 1 5 Environment Variables Coot responds to several environment variables that modify its behaviour N N o c Go COOT_STANDARD_RESIDUES The filename of the pdb file containing the standard amino acid residues in standard conformation COOT_SCHEME_DIR The directory containing standard part of the distribution scheme files COOT_SCHEME_EXTRAS_DIR A separated list of directories containing bespoke scheme files This variable is not set by default If you set it Coot will test each separated string that it points to a directory and if it does Coot will load all the scm files in that directory COOT_PYTHON_EXTRAS_DIR A separated list of directories containing bespoke python files This variable is not set by default If you set it Coot will test each separated string that it points to a directory and if it does Coot will load all the py files in that directory COOT_REF_STRUCTS The directory containing a set of high resolution pdb files used as reference structures to build backbone atoms from Ca positions COOT REF SEC STRUCTS The directory containing a set of high quality structures to be used as templates for fitting beta strands If this is not set then the directory COOT REF SEC STRUCTS will be used to find the reference pdb files COOT REFMAC LIB DIR Refmac s CIF directory containing the monomers and link de sc
303. turn 1 on failure Else return molecule number 11 8 25 screendump image Screendump image filename function Where filename is a string dump the current screen image to a file Format ppm You can use this in conjunction with spinning and view moving functions to make movies 11 8 26 set draw solid density surface set draw solid density surface imol state function Where e imolis an integer number e state is an integer number sets the density map of the given molecule to be drawn as a transparent solid surface 11 8 27 set draw map standard lines set draw map standard lines mol state function Where e imolis an integer number e state is an integer number toggle for standard lines representation of map This turns off on standard lines representation of map transparent surface is another representation type If you want to just turn off a map don t use this use 11 8 28 set solid density surface opacity set solid density surface opacity imol opacity function Where e imol is an integer number e opacity is a number Chapter 11 Scripting Functions set the opacity of density surface representation of the given map 0 0 is totally transparent 1 0 is completely opaque and because the objects are no longer depth sorted considerably faster to render 0 3 is a reasonable number 11 8 29 set flat shading for solid density surface set flat shading for solid density surface state function Where state
304. unction Where e molecule expression is a SCM e name is a string generate a molecule from an s expression return a molecule number 1 on error 12 7 3 clear and update molecule clear and update molecule molecule_number molecule expression function Where e molecule_number is an integer number e molecule expression is a SCM update a molecule from a s expression And going the other way given an s expression update molecule number by the given molecule Clear what s currently there first though 12 7 4 active residue active residue function return specs of the atom close to screen centre Return a list of list imol chain id resno ins code atom name alt conf for atom that is closest to the screen centre in any displayed molecule If there are multiple models with the same coordinates at the screen centre return the attributes of the atom in the highest number molecule number return scheme false if no active residue Chapter 12 More Seripting Functions 182 12 7 5 closest atom closest atom imol function Where mol is an integer number return the specs of the closest atom in imolth molecule Return a list of list imol chain id resno ins code atom name alt conf list x y z for atom that is closest to the screen centre in the given molecule unlike active residue no account is taken of the displayed state of the molecule If there is no atom or if imol is not a valid model molecule return scheme f
305. ur set background colour red green blue function Where e red is a number e green is a number e blue is a number set the background colour red green and blue are numbers between 0 0 and 1 0 11 59 2 redraw background redraw background function re draw the background colour when switching between mono and stereo 11 59 3 background is black p background is black p function is the background black or nearly black Returns 1 if the background is black or nearly black else return 0 11 60 Ligand Fitting Functions 11 60 1 set ligand acceptable fit fraction set ligand acceptable fit fraction f function Where f is a number set the fraction of atoms which must be in positive density after a ligand fit 11 60 2 set ligand cluster sigma level set ligand cluster sigma level f function Where f is a number set the default sigma level that the map is searched to find potential ligand sites 11 60 3 set ligand flexible ligand n samples set ligand flexible ligand n samples i function Where 1 is an integer number set the number of conformation samples big ligands require more samples Default 10 11 60 4 set find ligand n top ligands set find ligand n top ligands n function Where n is an integer number search the top n sites for ligands Default 10 Chapter 11 Scripting Functions 135 11 60 5 set find ligand mask waters set find ligand mask waters istate function Where istate is an integer number ho
306. urn a list of file names that match pattern pat in directory dir strip extension s a b res gt a b file name sans extension command in path cmd Return t or f goosh command cmd args data list log file name screen output also Where cmd is e g refmac log data list is list HEAD END Return the exist status e g 0 or 1 run command strings cmd args data list Return the strings screen output of cmd or f if command was not found string gt list of strings str Return a list if str is a string else return directory files dir The following functions from PLEAC guile version thereof of course or define a utility function for this add to list section texis delete section texi files procedure procedure procedure procedure procedure procedure refmac args is list HKLIN thing mtz log file name is procedure procedure procedure procedure procedure Chapter 13 Scheme Scripting Functions 212 13 39 tips gui show coot tip from list n text procedure given a number and a gtk text widget text put tip number n into the widget increment coot tip number procedure increment the tip number when the user sees a tip decrease coot tip number procedure decrement the tip number when the user sees a tip tips gui procedure run the tips gui 13 40 background demo background demo procedure flash the background different colours in some uninterest
307. urrently 12 13 Drag and Drop Functions 12 13 1 handle drag and drop string handle drag and drop string uri function Where uri is a const std string amp handle the string that get when a file or URL is dropped 12 14 Sectionless functions 12 14 1 ligand search make conformers scm ligand search make conformers scm function make conformers of the ligand search molecules each in its own molecule Don t search the density Return a list of new molecule numbers Chapter 13 Scheme Scripting Functions 185 13 Scheme Scripting Functions 13 1 redefine functions drag intermediate atom procedure scm aliases set find hydrogen torsion procedure fix typo of set find hydrogen torsions backward compatibility in case anyone was using that cif file for comp id procedure define residue gt sdf file residue to sdf file 13 2 jligand gui launch jligand function procedure This happens when user clicks on the Launch JLigand button It starts a jligand and puts it in the background click select residues for jligand procedure This happens when user clicks on the Select Residues for JLigand or some such button It expects the user to click on atoms of the two residues involved in the link 13 3 get recent pdbe coot thread dispatcher procedure coot thread dispatcher image name thunk dialog box of buttons with async ligands window name procedure geometry buttons close button label If check button
308. us of the generic display objects Chapter 11 Scripting Functions 171 11 92 12 generic object has objects p generic object has objects p obj_no function Where obj_no is an integer number does generic display object number obj_no have things to display predicate name Returns 0 for no things 1 for things 11 92 13 close generic object close generic object object number function Where object number is an integer number close generic object clear the lines points etc not available for buttons displaying etc 11 92 14 is closed generic object p is closed generic object p object number function Where object number is an integer number has the generic object been closed Returns 1 for yes 0 othersize 11 92 15 generic object clear generic object clear object number function Where object number is an integer number clear out the lines and points from object number but keep it displayable not closed 11 92 16 generic objects gui wrapper generic objects gui wrapper function a kludgey thing so that the generic objects gui can be called from a callback 11 93 Molprobity Interface 11 93 1 handle read draw probe dots handle read draw probe dots dots file function Where dots file is a string pass a filename that contains molprobity s probe output in XtalView format 11 93 2 handle read draw probe dots unformatted handle read draw probe dots unformatted dots file imol function show clash gui fla
309. users Return a list of models corresponding to the menu items of the option menu The returned list will not contain references to map or closed molecules fill option menu with number options menu number list procedure default option value get option menu active molecule option menu model mol list procedure Helper function for molecule chooser Not really for users return the molecule number of the active item in the option menu or return f if there was a problem e g closed molecule get option menu active item option menu item list procedure Here we return the active item in an option menu of generic items molecule chooser gui generic chooser label callback function procedure option menu fill function Typically option menu fill function is fill option menu with coordinates mol options Chapter 13 Scheme Scripting Functions 189 molecule chooser gui procedure Fire up a coordinates model molecule chooser dialog with a given label and on OK we call the call back fuction with an argument of the chosen molecule number chooser label is a directive to the user such as Choose a Molecule callback function is a function that takes a molecule number as an argument map molecule chooser gui procedure Fire up a map molecule chooser dialog with a given label and on OK we call the call back fuction with an argument of the chosen molecule number chooser label is a directive to the user such as Choose a Molecule ca
310. using gzip 11 14 Recover Session Function 11 14 1 recover session recover session function recover session After a crash we provide this convenient interface to restore the session It runs through all the molecules with models and looks at the coot backup directory looking for related backup files that are more recent that the read file Not very good because you need to remember which files you read in before the crash should be improved 11 15 Map Functions 11 15 1 calc phases generic calc phases generic mtz file name function Where mtz_file_name is a string fire up a GUI which asks us which model molecule we want to calc phases from On OK button there we call map from mtz by refmac calc phases Chapter 11 Scripting Functions 11 15 2 map from mtz by refmac calc phases map from mtz by refmac calc phases mtz_file name f_col sigf_col function imol_coords Where e mtz_file name is a string e f_col is a string e sigf_col is a string e imol coords is an integer number Calculate SFs using refmac optionally from an MTZ file and generate a map Get F and SIGF automatically first of their type from the mtz file Returns the new molecule number 1 on a problem 11 15 3 map from mtz by calc phases map from mtz by calc phases mtz filename f_col sigf_col imol_coords function Where e mtz_file name is a string e f_col is a string e sigf_col is a string e imol_coords is an integer number C
311. utating DNA RNA Mutation of DNA or RNA can be performed using Simple Mutate from the Model Fit Refine dialog Residues need to be named Ad Gr Ur etc 5 17 2 Multiple mutations This dialog can be found under Calculate gt Mutate Residue Range A residue range can be assigned a sequence and optionally fitted to the map This is useful converting a poly ALA model to the correct sequence Multiple mutations are also supported via the scripting interface Unlike the single residue mutation function a residue type match will prevent a modification of the residue Two functions are provided To mutate a whole chain use mutate chain imol chain id sequence where chain id is the chain identifier of the chain that you wish to mutate e g A and imol is molecule number sequence is a list of single letter residue codes such as GYRESDF this should be a straight string with no additional spaces or carriage returns Note that the number of residues in the sequence chain and those in the chain of the protein must match exactly i e the whole of the chain is mutated except residues that have a matching residue type To mutate a residue range use e mutate residue range imol chain id start res no stop res no sequence where start res no is the starting residue for mutation stop res no is the last residue for mutation i e using values of 2 and 3 for start res no and stop res no respectively will mutate 2 r
312. w shall we treat the waters during ligand fitting pass with istate 1 for waters to mask the map in the same way that protein atoms do 11 60 6 set ligand search protein molecule set ligand search protein molecule imol function Where mol is an integer number set the protein molecule for ligand searching 11 60 7 set ligand search map molecule set ligand search map molecule imol map function Where mol map is an integer number set the map molecule for ligand searching 11 60 8 add ligand search ligand molecule add ligand search ligand molecule imol ligand function Where mol ligand is an integer number add a rigid ligand molecule to the list of ligands to search for in ligand searching 11 60 9 add ligand search wiggly ligand molecule add ligand search wiggly ligand molecule imol ligand function Where mol ligand is an integer number add a flexible ligand molecule to the list of ligands to search for in ligand searching 11 60 10 ligand expert ligand expert function this sets the flag to have expert option ligand entries in the Ligand Searching dialog 11 60 11 do find ligands dialog do find ligands dialog function display the find ligands dialog if maps coords and ligands are available that is 11 60 12 match ligand atom names match ligand atom names imol ligand chain id ligand resno ligand function Ins code ligand imol reference chain id reference resno reference ins_code_reference Where Chapter
313. ward direction defaults to 1 Chapter 5 Modelling and Building baton atoms build in the opposite direction are not dependent on the first few atoms of the previously build fragment 5 8 Reversing Direction of Fragment After you ve build a fragment sometimes you might want to change the direction of that fragment this function changes an already existing fragment as opposed to Backwards Building which sets up Baton Building to place new points in reverse order The fragment is defined as a contiguous set of residues numbers So that you should be sure that other partial fragments which have the same chain id and that are not connected to this fragment have residue numbers that are not contiguous with the fragment you are trying to reverse 5 9 C alpha gt Mainchain Mainchain can be generated using a set of Cas as guide points such as those from Baton building along the line of Esnouf or Jones and coworkers Briefly 6 residue fragments of are generated from a list of high quality structures The Ca atoms of these fragments are matched against overlapping sets of the guide point Cas The resulting matches are merged to provide positions for the mainchain and C atoms This procedure works well for helices and strands but less well for less common structural features This function is also available from the scripting interface db mainchain imol chain id resno start resno end direction where direction is either
314. with guile Le function argl arg2 If you are using Python instead the format needs to be changed to function argl arg2 Note that dashes in guile function names become underscores for python so that for example raster screen shot becomes raster screen shot O 3 10 2 Scheme The scheme interpreter is made available by embedding guile The initialization script used by this interpreter is HOME coot This file should contain scheme commands that set your personal preferences 3 10 3 Coot State The state of Coot is saved on Exit and written to a file called 0 coot state scm scheme 0 coot state py python This state file contains information about the screen centre the clipping colour map rotation size the symmetry radius and other molecule related parameters such as filename column labels coordinate filename etc 7 which causes the evaluation of the command 8 such as the Coot state file Section Section 3 10 3 Coot State page 12 Chapter 3 General Features 13 Use Calculate gt Run Script to use this file to re create the loaded maps and mod els that you had when you finished using Coot last time A state file can be saved at any time using save state which saves to file O coot state scmor save state filename thing scm which saves to file thing scm When Coot starts it can optionally run the commands in 0 coot state scm Use set run state file status i to change the behaviour
315. zr function Where e risa number e y is a number e zisa number e risa number return the closest text that is with r A of the given position If no text item is close then return 1 11 103 PISA Interaction 11 103 1 pisa interaction pisa interaction mol imol_2 function Where e imol 1 is an integer number e imol 2 is an integer number return the molecule number of the interacting residues Return 1 if no new model was created Old not very useful 11 104 Jiggle Fit 11 104 1 fit to map by random jiggle fit to map by random jiggle imol chain_id resno ins_code n trials function jiggle scale factor Where e imolis an integer number Chapter 11 Scripting Functions 176 e chain_id is a string e resno is an integer number e ins code is a string e n irials is an integer number e jiggle scale factor is a number jiggle fit to the current refinment map return 100 if not possible else return the new best fit for this residue 11 105 SBase interface 11 105 1 get sbase monomer get sbase monomer comp id function Where comp id is a string return the new molecule number of the monomer The monomer will have chainid A and residue number 1 Return 1 on failure to get monomer 11 106 FLE View 11 106 1 fle view set water dist max fle view set water dist max dist max function Where dist max is a number set the maximum considered distance to water default 3 25 A 11 106 2 fle

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