L01: Desktop Molecular Graphics PyMol 1
Contents
1. 6 PyMol Exercise F Clipping planes amp distance measurements 6 1 Clipping planes Clipping planes are imaginary planes in the front and back of the molecule Parts of the molecule that are outside the planes are clipped and therefore invisible This is very useful for complex or large structures This image represents the molecule seen side ways inside the computer monitor The 2 black lines represent the yon mG far away and hither close clipping ki planes These are parallel to the flat screen of the computer monitor display The gray lines converge d toward the user s eye who is looking bar yon at the molecule on the computer screen d TASK The DMC computers are equipped with 3 button mice To move clipping planes press shift and the right mouse button simultaneously while dragging up and down The same result can be obtained by using the middle button scroll wheel As an exercise try to remove some of the molecular surface covering the ligand to create a picture similar to this UR T Een an Note we have seen previously that the top menu Mouse contains all the possible options with a reminder displayed at the bottom right of the Internal GUI The method to adjust the clipping plane will depend on the number of buttons on your mouse Use the Mouse menu to adapt your display to your mouse Depending on the mouse viewing option See exercise above about choosing2. gt MClear V autopick Rings L A EJ E K D Command Builder autozoom Charge 1 0 1 Bond Create Delete valence Editing FixH AddH Invert Center Delete Clear Protein builder panel Chemical Ala 4sp sn Arg Cys Glu Gln Gly His lle Leu Lys Protein Met Phe Pro Ser Thr Trp Tyr Val Ace lt gt MClear autopick Secondary Structure Next parallel beta sheet Command Builder autozoom Charge 1 0 1 Bond Create Delete yalence Editing FixH AddH Invert Center Delete Clear ETA AEGEE IS Via the i menus Chemical molecules builder panel Protein builder panel Build Movie Display Setting Scene Mouse Wizard Help Movie Display Setting Scene Mouse Wizard _H es ee P gt l Fragment p WARK Residue eee tannin Acetyl Opt J Amide N gt C Opt 1 a Alanine Opt A Amide C gt N Opt 2 z Sculpting P Amine Bromine Ctrl B Cycle Bond Valence Ctri W Aspartate Opt D Cycle Bond Valence Ctrl W Carbon Ctrl C Fill Hydrogens on pk1 Ctrl R Asparagine Opt N Fill Hydrogens on pk1 Ctrl R Carbonyl Opt O Invert pk2 pk1 pk3 Ctrl E Arginine Opt R Invert pk2 pk1 pk3 Ctrl E Chlorine Ctrl L Create Bond pk1 pk2 Ctrl T gt nena Opt C utamate Opt E Create Bond pk1 pk2 Ctrl T Cyclobutyl Opt 4 Remove pk1 Ctrl D Glutamine Opt Q Remove pk1 Ctrl D Sculpting Cyclopentyl Opt 5 Glycine Opt G Cyclopentadienyl Opt 8 Make pk 1 Posi
3. Zoom Draw J Ray i Rock Unpick Hide Sele Get View i lt X lt y Stop Play gt J gt MClear Type the next commands after PyMOL gt within the top line command 41 d TASK PyMOL gt cd desktop PyMOL gt cd desktop Note the echo on the text area above PyMOL gt pwd this will echo Users DMC Desktop ora similar path On a Windows system the path would begin with C Note PyMol uses many Unix commands cd change directory pwd present working directory PyMOL gt load 2BIW pdb2 PyMOL gt load 2BIW pdb2 HEADER OXIDOREDUCTASE 19 JAN 05 a XXXX This will load the structure TITLE CRYSTAL STRUCTURE OF APOCAROTENOID and echo information in the CLEAVAGE OXYGENASE FROM text panel as reproduced to TITLE 2SYNECHOCYSTIS NATIVE ENZYME COMPND APOCAROTENOID CLEAVING OXYGENASE ObjectMolecule Read secondary structure assignments ObjectMolecule Read crystal symmetry information Note file name is case sensitive Symmetry Found 4 symmetry operators CmdLoad 2BIW pdb2 loaded as 2BIW pdb2 the right Note XXXX substituted for 2BIW within the saved PDB text because we opted to select only a portion of the original PDB data when we chose to use a biological subunit rather than the complete entry The XXXX reflects that this is a partial or altered PDB file Note why not use the File gt Open menu Open sequence Good question You can actually try that option and
4. Auto Remove Hydroger Setting gt Auto Zoom New Objects OW 11 PyMol Exercise K Side chain mutations PDB files show the structure of a particular sequence and conformation However sometimes it is useful to mutate a side chain to see what the effect might be 11 1 Preliminary create a standard view to work with Y TASK actions orient 2BIW db center y Follow the menu cascades tee Preset drag i simple preset 2BIW pdb2 a A a preset gt ligand simple no solvent Find stes gt transparent ball and stick align Ib factor putty renerate This will create a similar view of the ei pea eee rename object i i i ST J ligand within the pocket with some ETET EE Pe eae r s soli etter pretty with solvent amino acid sides chains shown as solad bett a AE hydrogens publication with solvent Temove waters default State masking sticks transparent better dot surface mesh surface sequence 72 BM Biochem 660 2008 The default colors are rainbow To make the display clearer change the ay T colors with the following cascade TA 7 ob 01 menus 2BIW pdb2 gt C gt blues gt slade y Click on the ligand y sele gt C gt yellow 1 1 23 se lt m gt pfs 11 2 Select side chain to mutate Since we already worked with Tyr 322 above we shall use this as an example Y TASK Rotate the view to find Tyr 322 y Click within the blank ar
5. Note the file has a binary format There is no information within the file that is useful for any other purpose The file for this exercise should likely be slightly less than 1Mb in size KA KA AN A 9 PyMol Exercise l Electrostatic potential The most accurate potential maps can be calculated by external software Grasp Delphi APBS MEAD and displayed in PyMol A tutorial example for APBS is available online at http www bio3d igbmc u strasbg fr doclib apbs tutorial index html PyMol offers an approximate map nicknamed Vacuum Electrostatics charge smoothead surface representing Prete Genesee O era approximate charge distribution on the protein ero ean Ee Cee SR res r OR i lack of solvent screening these con surface Assuming that you have opened PDB file 2BIW pdb2 the potential surface is calculated and displayed with the following menu cascade on the Names Panel potentials are only qualitatively usel Please view with skepticism Note for reading clarity colors are inverted 9 1 calculating and displaying a map Biochem 660 2008 TASK NN 2biw pdb2 fal site ic he kso ss FB Fi ae eS ha j N iw e 2BIW pdb2 gt A gt a R a generate gt vacuum electrostatics gt protein contact potential local The process Box Box Clip Movs eae ow gt A a entries within the PKA Names Panel 2BIW pdb2 e ch g 2BIW pdb2 e ma p and 2BIW pdb2 e pot 2BIW pdb2
6. mouse viewing it may be necessary to use different mouse keyboard strokes When the mouse option is changed the bottom right panel of the graphical GUI changes V iNFO Changing mouse options review 1 button mouse viewing Wizard Help l Selection Mode 3 Button Viewing Mode R 0 ta 3 Button Editing Mode B Ox 2 Button Viewing Mode M Ove 2 Button Selecting Mode L li 2 Button Editing Mode t7 1 Button Viewing Mode Menu v Virtual Trackball i 1 1J 2 button mouse viewing 3 button mouse viewing a Move Mov Slab x Box Clip Movs PkAt Pki My TAT h l m4 Cent Menu PkKAt Moved PkAt Lent Menu Lent t al love iz Ht Pk Ro PH M m Z N 7 d do on y a WH M Nf moe f 1 O sec Biochem 660 2008 Regardless of the number of buttons on your mouse simply look at the bottom right to see the corresponding mouse keyboard action for the following 2 items MovZ and Clip MovZ will move the object closer or further from your point of view Clip will reduce the size of the box into which the object is represented and increase the contrast with depth cueing making parts of the molecule that are further back much darker Playing with these 2 items it is possible to increase the feeling of depth and 3D feeling of any represented object and particularly surfaces with deep pockets You need to make sure however that the the depth cue option is engaged
7. y Click on Protein button far left Change the default parallel beta sheet to helix bottom of menu Click next twice Protein Met Phe Pro Thr Trp Ty Met Phe Pro Ser Thr Trp V autopick Secondary Structure Nests par allel beta sheet Secondary Structure Next alpha helix Click on Ala 12 times The model will be built within the Viewer and have name ala within the Names Panel d Save the molecule into a file y menu File gt Save Molecule verify that ala is selected or click on ala Click OK y The default name is the name of the first amino acid used e g ala pdb The alpha helix is created as a perfect model and contains all hydrogen atoms 13 PyMol Exercise M Displaying hydrogen bonds d INFO See also Polar Contacts within the following web page http www pymolwiki org index php Displaying_Biochemical_Properties In the previous exercise we created a short a helix which we will use here for illustration 13 1 Example 1 short helix model It will be easier to display and see the hydrogen bonds if the hydrogen atoms are removed d TASK y Remove hydrogens with the menu cascade within the Names panel Find align generate preset assign sec struc ala gt A gt hydrogens gt remove ears gest duplicate object ydrogens t delete object add remove waters Biochem 660 2008 To display hydrogen
8. To restore it simply click on button 2BIW pdb2 within the Names Panel this will restore the display of the protein and ligand as lines or sticks Since the protein is under the surface it will remain invisible but some odd side chains might stick out of the surfaces To make more complex images it may be useful to create a new object containing the ligand alone see creating objects below 9 6 Deleting the calculated maps 2BIW pdb2 e chg 2BIW pdb2 e map and 2BIW pdb2 e pot are PyMol objects that can be deleted with the A action button Note the menu will be different for the 3 objects within the A menu d TASK Delete the 3 objects pertinent to the electrostatic potential 2BIW pdb2_e_chg gt A 2BIW pdb2 e map gt A 2BIW pdb2 e pot gt A gt gt delete gt delete delete 2bivs pab2_e_map lace ions fll BIWBEDSNEL BEEN a one Be Pot nesh P P Actions surface delete preset find align generate assign sec struc rename object duplicate object delete object 10 PyMol Exercise J Creating new objects automatic zooming 10 1 Making a new object from selection The current selection sele as well as other subsets are shown within parentheses and represent subsets of the current PDB file we are working on e g 2BIW2 pdb2 Any selection can be copied into an independent object with the A Actions copy to object menu cascade This will create a new entry within the Names Panel withou
9. Z axis left click on the top left or right corner Translate move sideways X or Y click middle button and drag Zoom move along Z axis click right button and drag up or down 3 3 Changing the default mouse settings Mouse Wizard Help of INFO l Selection Mode gt By default PyMol assumes that you have a 3 button T dimen EM EdE mouse If you have a 2 or one button mouse you can ORES AEs coir change the setting accordingly with the Mouse menu in the top menu bar oS os Note the updating of the Mouse Mode button mapping sao at the bottom right within the Internal GUI if you change the mouse setting Wizard Help Selection Mode gt Atoms Note the Selection Mode gt submenus define what is See selected when an atom is clicked on 3 buton baiting Mede E nen 2 Button Selecting Mode Objects 2 Button Editing Mode Molecules The selection default is Residues 1 Button Viewing Mode C alphas Virtual Trackball 3 4 Show menu S Changing the representation style of the molecule a READ PyMol can open more than one molecule at a time or separate complex PDB files into individual components Each opened or loaded molecule is given a name within the Names Panel see picture above The first name is always all Clicking on the name itself will undisplay the corresponding molecule s temporarily invisible Biochem 660 2008 The ASHLC menu Als H L lig is abbreviated for Acti
10. be either orange or the color for loops in the C ss Helix Sheet Loop color scheme chosen in the step above 3 8 Surface representation Surface representation used to be extremely computationally intensive However PyMol offers very fast and beautifully rendered surfaces eS 7 A Li Hide SY TASK 4 everything Using the show S menu display the surface of the protein then hide it a with the H menu dots spheres nb_spheres 2BIW pdb2 gt S gt surface main chain side chain _ 0 sec 2ZBIW pdb2 gt H gt disulfides Mea ie 2 MERGA surface 3 9 Mouse selection Now that we have made the ligand visible it becomes easier to select it with the mouse to make further changes A TASK Click on one of the spheres of the carotenoid ligand This simple click makes various things happen e pink square dots appear onto all the spheres of the ligand indicating that it has been selected e A new name line appears within the Names Pane GUI called sele and is now dedicated to this subset of atoms Note that the content of sele changes as other atoms are clicked The name of the atom that was clicked appears within the top text window of the external GUI For example You clicked 2BIW pdb2 B TYR 322 0H Selector selection sele defined with 12 atoms This could be read as you clicked atom OH which is on the 322 atom in the file and belongs to Tyrosine 322 of chain B in
11. for slide presentations but is still one step short of the quality needed for high resolution publication as the image created by the default setting is the same size as that of the current Viewer default size is 640 x 480 pixels when PyMol is first opened The default file format is the new PNG standard All we need to do at this point is change the default setting of the ray traced file size Y TASK Biochem 660 2008 Within the PyMOL gt line hel ee command type the ror TE an coc 220 6 following command to pyuou gt ray 2000 2000 0 change the dimensions of crence nour 56 02 sec accua j 7 the final ray traced image PyMOL gt ray 2000 2000 ray 2000 2000 2000 is an example number Note the comma between the two numbers The higher the numbers the longer it will take to compute the image PyMol will display the size of the calculated image within the Viewer under the image here 2000 x 2000 Image size 2000 x 2000 Note ray 2000 typed within the line command input is also a valid command In this case PyMol will evaluate the missing value and adjust it to minimize the file size A INFO Ray tracing options There are 50 editable settings listed in the menu Setting gt Edit All for ray tracing The following 2 are of special interest ray_shadows is on and can be edited within the settings window or the line command set ray_shadows on or set ray_shadows off ray_tra
12. is subsequently abbreviated X below X_e_chg is an object containing the surface colored red white blue and is an approximate map X_e _map is usually not shown click on name to show and displays the volume boundaries as e g a big cube X_e_ pot is the object representing the color ramp and value at the bottom of the display 9 2 Adjusting color levels with the mouse With protein 2BIW the default values for red and blue are 55 248 and 55 248 respectively It is possible to adjust the color level with the middle button and the control key Y TASK Place the mouse over the color scale y Hold the CTRL key and click on the middle button Adjust the color level by sliding the middle button Go first to a range near 100 y Then to a range near 10 T I MIN 67 Note Do not go all the way to 0 0 as it then becomes virtually impossible to slide to proper values after that 9 3 adjusting the value range and color strength with line command If two proteins are present the process has to be applied to each individual protein and the same __e_ objects are created for each one The values within the X_e_pot color ramp may be different for each protein Therefore it is useful to know how to change the values within Smaller numbers will increase the blue and red strength and contrast within the blend of white surface while larger numbers will dim the colors Vd TASK To change the color range
13. preset menu cascades with the suggested colorings 2BIW pdb2 gt A gt preset gt ligand sites gt solid surface 2BIW pdb2 gt C gt yellows gt sand y Click on the ligand to obtain a selection sele that contains it y sele gt C gt blues gt slate 5 1 Sequence viewer The molecule sequence can be shown at the top of the graphical area d TASK To engage sequence viewing follow the top menu cascade Display gt Sequence on The sequence appears just below the PyMOL gt line command at the top of the Viewer The slide cursor underneath can be used to move the sequence viewed further l 2BIW pdb27 B7 12 16 21 26 31 36 41 46 at 56 61 66 71 76 ORSYSPODWLRGYOSOPOEWDYWVEDVEGSIPPDLOGTLYRNGPGLLEIGDRPLKHPFOGDGMYTA By default the one letter code is displayed Setting Scene Mouse Wizard _ v Sequence On L Since we are looking at a protein changing the TOTTI Residue Codes display to the three letter code will be useful Stereo On Residues l within the next step Aereo r BB c Zoom gt Sead vA TASK Chip a States Display gt Sequence Mode gt Residues With the mouse rotate the molecule to a view similar to that shown at right With the mouse click on the tyrosine residue under the right hand side which contribute to the pocket surface Change it s aspect to stick with the following menu cascade sele gt S gt sticks eS 57 Note When you clicked the following text appeared wit
14. viewer is 640 x 480 pixels MacPyMOL File Edit Build Movie Display Setting Scene Mouse Wizard Help Note The menu bar might be attached to the external GUI in other systems By default PyMol will display the molecule s contained within the PDB file as a wireframe This cyanobacterium molecule is a carotenoid oxygenase and contains a carotenoid ligand 3 1 PyMol settings to work on ave Y INFO The Display gt Quality menu cascade allows you to adapt to the speed of you machine CPU depending on the quality of the image displayed in the Viewer slow laptop computer Display Maximum Performance Reasonable Performan Reasonable Quality Maximum Quality Orthoscopic View Use Display Lists Shaw Vialancac This option MAY affect the result of ray traced images Ray traced images are explained below The DMC computers are recent and powerful However if you are using PyMol on a slow computer or very slow laptop choose the Maximum Performance to work faster 3 2 Mouse control of the 3D representation The 3D molecule is represented within a virtual 3D world The flat surface of the screen represents the X and Y axes while the Z depth axis is perpendicular to the screen PyMol is optimized for a 3 button mouse but most basic functions can still be achieved by a one button mouse in particular the rotations around X Y and Z Rotation around the X or Y axis left click and drag Rotation around the
15. within the menu Display 6 2 Measuring distances with the Measurement Wizard Distances are measured between two atoms and are expressed in the same unit as the XYZ coordinates within the PDB file Angstroms 1A 107 m As an example we shall measure the distance between two atoms within the carotenoid ligand Within the top menu select Help Note In older PyMol versions Measurement was called Distance This will create a prompt within the Viewer Please click on the first atom Within the Internal GUI a Measurement table also appears It can also be used to remove measurement objects after they are no longer needed Click on the first atom on the ligand Click on the second atom on the ligand you can select the same atoms as in the examples within the image at right or select your choice of atoms The default color of the measurement object is yellow This can be easily changed with the familiar ASHLC menu for each measurement as a new name is entered within the Names Panel for each distance e g measure01 Change the color to white with the following menu cascade measure01 gt C gt grays gt white Quiz exercise you can also measure the distance between the OH at the tip of TYR 322 and the nearest ligand atom C30 Answer When you are done using the Measurement panel on the bottom right click Done If you no longer need to display the distance o
16. within the ramp example ramp new 2BIW pdb2 e pot 2BIW pdb2 e map 100 0 100 9 4 Adjusting the display colors The default colors are red white blue hence the above command could also be rewritten to change ramp values and specify colors ramp_new 2BIW pdb2_e_ pot 2BIW pdb2_e map 100 0 100 red white blue or ramp_new 2BIW pdb2_e_ pot 2BIW pdb2_e map 100 0 100 1 0 0 1 1 1 0 0 1 where 1 0 0 1 1 1 0 0 1 represents the R G B red green blue channels values for each of the 3 displayed colors To change the displayed color simply change the definition of the colors For example the values 1 1 0 1 1 1 0 1 1 would create a ramp as yellow white cyan Biochem 660 2008 of INFO Edit All 000 mrem Cartoon Ribbon An alphabetical list of all ldai T PyMol defined color names Ignore PDB Segment Identifier v Auto Zoom New Objects Can be fou nd under the top v Auto Show New Selections ct 3 v Auto Hide Selections menu Setting gt Colors TE Auto Remove Hydrogens Show Text i s 3 Hide Text Within that window the colors Overlay Text can also be edited The C menu within the Names Panel offers a list of color names grouped by tint and can serve as a preview 9 5 Default display Note that when the calculation first takes place the surface is shown but the original PDB file is hidden In the case of 2BIW it means that the carotenoid becomes invisible
17. ASK Explore the L menu knowing that clear will remove the mess that may occur on this image colors were inverted for easier reading 7 3 General label Settings General default settings can also be altered generally oS TASK De mF Label clear residues chains segments atom name element symbol residue name residue identifier chain identifier segment identifier b factor occupancy vdw radius other properties atom identifiers Open the Setting gt Edit All top menu and change settings as illustrated Default label values Label values changed Setting isomesh_auto_state label_angle_digits label_color label_digits label_dihedral_digits label_distance_digits label_font_id label_outline_color label_position label_shadow_mode label_size legacy_mouse_zoom 7 4 Labeling one atom Setting isomesh_auto_state label_angle_digits label_color label_digits label_dihedral_digits label_distance_digits label_font_id label_outline_color label_position label_shadow_mode label_size leqacy_mouse_zoom Text label can also be added within PyMol although as suggested above adding label within a graphical software might be more appropriate in some cases vA TASK Mouse Wizard Help Change the mouse selection to Atoms Click on one atom within the carotenoid Will show pink square Within the text entry box type the following command PYMOL gt label sele Ligand x lab
18. AVAGE RETINAL KEYWDS 2 FORMATION OXIDOREDUCTASE DIOXYGENASE EXPDTA X RAY DIFFRACTION AUTHOR D P KLOER S RUCH S AL BABILI P BEYER G E SCHULZ JRNL AUTH D P KLOER S RUCH S AL BABILI P BEYER G E SCHULZ JRNL TITL THE STRUCTURE OF A RETINAL FORMING CAROTENOID JRNL TITL 2 OXYGENASE JRNL REF SCIENCE V 308 267 2005 JRNL REFN ASTM SCIEAS US ISSN 0036 8075 REMARK 1 SEQRES 1A 490 MET VAL THR SER PRO PRO THR SER SER PRO SER GLN ARG SEQRES 2 A 490 SER TYR SER PRO GLN ASP TRP LEU ARG GLY TYR GLN SER ecole ee ee T eee MTRIX2 3 0 756169 0 514705 0 404088 13 98510 iL MTRIX3 3 0 610627 0 777006 0 152957 118 86930 1 ATOM 1 N GLNB 12 16 794 17 939 28 900 1 00 71 25 ATOM 2 CA GINB 12 16 091 17 967 30 218 1 00 71 00 ATOM 3 C GINB 12 16 877 17 181 31 273 1 00 69 76 a en E ee es ATOM 3766 CG2 THR B 490 47 002 0 207 59 451 1 00 73 42 ATOM 3767 O THR B 490 48 633 0 228 56 341 1 00 73 10 TER 3768 THR B 490 HETATM 3769 FE FE B1492 30 259 6 403 38 822 1 00 45 64 HETATM 3770 O1 30N B1491 26 391 21 062 36 210 1 00100 47 HETATM 3771 C5 30N B1491 25 099 20 591 36 637 1 00100 23 ee ee ee CONECT 3799 3798 CONECT 3800 3798 3801 CONECT 3801 3800 MASTER 0 0 0 36 154 0 24 1515742 4 37 152 END aaz 2 PyMol Exercise B Open PyMol and load PDB file Note Some versions of PyMol have the top and bottom panels in separate windows but TASK double click on the PyMol icon to launch the software offer the same interfa
19. Biochem 660 2008 L01 Desktop Molecular Graphics PyMol 1 From the preface of the User s guide PyMOL was created in an efficient but highly pragmatic manner with heavy emphasis on delivering powerful features to end users Expediency has almost always taken precedence over elegance and adherence to established software development practices is inconsistent PYMOL is about getting the job done now as fast as possible by whatever means were available PyMol is a multiplatform molecular graphics software with many advanced features such as rendered cartoon ribbons and surfaces internal ray tracing and movie tools and is fast becoming the new standard in molecular graphics The PyMol web site is located at http pymol sourceforge net Biochemistry students can download the latest PyMol version from a campus network at http www biochem wisc edu it resources aspx Note within the exercises Bold text shows what actions are taken by the user typing text or clicking the mouse Whenever possible a call for action icon V or A will be shown OW FE 1 PyMol Exercise A Download a PDB from the repository Reminder Structures have a PDB ID code made of 4 letters and numbers PDB files contain coordinates pertinent to the crystallographic arrangement of the molecules within the crystal The biological functional entity can be either a multimer of the deposited structure or just one of multiple copies
20. X11 Applications Edit Window Help 90 e xterm bash 3 2 e080 X The PyMOL Molecular Graphics System File Edit Build Movie Display Setting Scene Mouse Wizard Plugin Chemical Atoms c n o P s F _a amp Protein Fragments CH4 C C C C NC 0 C 0N c 0 S 02 E autopick Rings Olle lolole se i autozoom Charge o 1 Bond Create Delete I cycle valence Editing Fix H Add H Invert Center Delete Clear Protein builder panel Chemical Ala Asp Asn Arg Cys Gu Gin Giy His ie Met Phe Pro Ser Thr Trp Tyr Val Ace E autopick secondary Structure Next parallel beta sheet Protein autozoom Charge A OF 1 Bond Create Delete _ valence Editing Fix H Add H Invert Center Delete Clear 12 1 Steps to build a poly Alanine model helix a Macintosh MacPyMol follow lt EEN the menu cascades x nn NF 4 ternet aisimi ig Build gt Residue gt Helix WA UIAA OOS j RLO IF Build gt Residue gt Alanine oS Repeat another 11 times for a Y total of 12 residues y Alternatively use the Option A keyboard shortcut The model will be built within the Viewer and have name ala within the Names Panel Note the C carbon to which the next amino acid is attached is shown by a spherical symbol c Windows X11 y Click on Builder button far right
21. aging the option Smooth Loops will simplify the drawing Removing the option Highlight Color will make the edges of strands and inside helices surfaces a gray color default vA INFO Cartoon Options Turning the variable cartoon_discrete_colors Setting on makes the helix color end abruptly at the Edit All ends of the helix The default value is off The eee change can be done manually with the menu cascade Setting gt Edit All or can be given se cat helices 0 as a typed command set cartoon_discrete_colors on the blank space on either side of the sign is optional set cartoon_discrete_colors off set cartoon_discrete_colors on Settings 3 6 Background color Black backgrounds look very nice on the screen but do not print well on paper and do not photocopy well Changing the background to white is usually very useful The Display menu within the top menu bar Sethe ente Mourners S O untitied Tol contains options for most options pertinent to eee ee displaying the image witin the PyMol viewer ae gt Zoom p VA Clip Pe asic To change the background color to white follow this Color Space gt Light Grey menu cascade a Io Orthoscopic View o Use Display Lists Display gt Background gt White e a moo Ines v Depth Cue Note that there is fog within the back of the Se ad desl y Specular Reflections molecule which can be toggled on and off with the Depth Cue menu item
22. bject click Delete All Measurements Alternatively you can use the corresponding A menu and select the delete option SY INFO Distances are labels The display of a distance measurement is a label To alter the number of decimal digits reported change the label setting label_ digits from default 1 to the desired value with either the Setting gt Edit All menu cascade or the line command set label_ digits 2 7 PyMol Exercise G Labels 7 1 Labels vA TASK Click on TYR 322 to have it within the sele name A label containing the residue type and sequence number e g TYR 322 can be added to a selected residue with the menu cascade sele gt L gt residues By default labels are created the same color as the atom 7 2 Label color How can I change only the label color without changing the display of the atom or molecule You can change the label color to e g yellow with the following line command Biochem 660 2008 set label_color yellow sele e Yellow can be changed for other colors The C menu can be a source of inspiration for colors and color names e sele represents the current selection You can alter the command with the name of the object you are working on e g 2BIW pdb2 e note the use of the comma within the line command For publications or slide making labels could be added with e g Adobe PhotoShop Illustrator or Microsoft PowerPoint graphic editing software wv T
23. bonds follow the menu cascade from the Names panel ala gt A gt find gt polar contacts gt within Grr eT selection ee eee excluding solvent sec s Note the bonds are shown as yellow a tara cee Lea Senn dashed lines which can be changed toa perariosmsseirit delete object darker color with the C Names panel T eS ay Pa ener button eet eee rte Note the polar contacts are created under the entry named ala_polar_conts within the Names panel and this button can be clicked to toggle the display of the bonds on and off y Click on all within the Names panel to render all displays invisible as a preparation for the next exercise below 13 2 Example 2 helix segment within 2BIW pdb2 d TASK y load the 2BIW pdb2 file one more time Within the Names panel 2BIW pdb2 gt H gt everything The following is an example to display the hydrogen bonds within the alpha helix consisting of residues 94 to 105 in 2BIW pdb2 y First create object helix 1 containing the helix residues by typing the following line within the line command area this type of command and its syntax will be reviewed in details in the next lab select helix 1 resi 94 105 y Display the selection Names panel helix 1 gt S gt sticks eS 79 For easier rotation enter the line command center helix 1 y Then find the polar contact the menu cascade from Names panel helix 1 gt A gt find gt polar contact
24. ce A current PyMOL Maintenance and or Support Subscription may be required for legal use of this Build beyond a finite honor system evaluation period Please visit http www pymol org funding html for more information About MacPyMOL MacPyMOL PyMOL Enhanced for Mac OS X Copyright C 2006 DeLano Scientific LLC pee lz a yer Incentive oa Itis not Plea of this software in your workplac You may evaluate Mac eee u ite time via the honor system saa that you must mainta a PyMOL su iese cription in order to acPyMOL in aca d me government or commercia ial researc h activities To pes ndjor 258 subscription visit http ome pymol o roe pe ng html est a price quote via email from sales dels NOTICE If at lea MacPyMOL wit hau pees conditi then you may optio nally u 2 PyMOL subscription an d wath out su ppi ort or maintenance services If you are a full time student only using MacPyMOL to teach students n preparation for teaching uch as rasa rubli c databas If you only u ait re or jew pre g public oraa PDB entries published si publicy able e PyMOL s akyon only usi he Aide JOL to dew and market your own computer hardware Smear ol oducts that work with Mac cPyMOL For general information about PyMOL visit http www pymol org PyMol or MacPyMol should be located within Applications gt Classes on the DMC computer Your instructor may give you a different location if necessary Reset
25. ce_mode has a default of 0 and can also adopt values of 1 and 2 to create contour enhanced images or old fashion black and white contours in the Jane Richardson style that used to be hand drawn set ray_trace_mode 1 set ray_trace_mode2 To render type ray or click ray button Return to ray trace defaults set ray_trace_mode 0 3 12 Where is the HELP command SY READ 3 12 1 Web help Some on line web content can be called from the Help menu in PyMol The default web browser is opened and content is displayed PyMol Wiki http pymolwiki org index php Main_Page with links to other PyMol Wikipedia pages PyMOL Mailing List PyMol Mailing List opens the mailing list subscribe page and PyMOL Home Page offers links to archives Purchasing MacPyMOL PyMol Home Page opens http pymol sourceforge net Sisal S TEONE Citing MacPyMOL 3 12 2 Documentation Older PyMol User s Manual and Pymol Reference Manuals are available online as HTML or PDF http pymol sourceforge net html Biochem 660 2008 Newer documentation can be accessed for authenticated users any connection from UW campus at http delsci info dsc dokuwiki doku php 3 12 3 Internal help PyMol also offers an internal summary of all the command derived from the manual These are called from the line command help xxx where xxx is the name of the line command e g help alignorhelp color The information displayed is essentially that of the refer
26. domains in separate rainbow colors and shows backbone and side chains technical Note that a subset name appears in the Names Panel 2BIW pdb2_pol_co that control the dashed line hydrogen bonds pretty and publication create similar images of a rainbow color cartoon with a stick ligand Pretty creates the default cartoon setting while publication creates an image very similar to an image created by Molscript Per J Kraulis 1991 MOLSCRIPT A Program to Produce Both Detailed and Schematic Plots of Protein Structures Journal of Applied Crystallography 24 946 950 http www avatar se molscript ligands This option will zoom in on the ligand site and show the protein as backbone except in the near vicinity of the ligand where side chains are shown The ligand is depicted as a thicker cylinder Note to zoom out simply click on the A in the ASHLC menu again PuMOL gt J XA i s y ligand sites A Prasat 7 simple l l l x Seesimple no Asiar There are a few options available in this gt oa ie submenu all pertinent to looking closely at the om technical i i T Ligand Sites ligands ligand In It S binding pocket cartoon ligand sites solid surface pretty A PRERE TTE pretty with solve You can explore a few of them on your own once memener O you are done then select the following option transparent better publication with preset gt ligand sites gt solid surface O Gasca z
27. ea to un select previous sele y Click on Tyr 322 with the mouse to select it Change it to red sele gt C gt reds gt red note that the surface associated with y Tyr 322 will also change color na 11 3 Mutagenesis Wizard The menu cascade Wizard gt Mutagenesis opens a new panel below the Names Panel and above the mouse control reminder Directions will be prompted with text overlaid on the Viewer MOEREN and AARMA pick a new residue f TASK Steps to mutate one amino acid side chain on a protein structure PyMol1 73 e Open from the menu Wizard gt Mutagenesis EEN Help Appearance Measurement Mutagenesis When GiSMEMcerei appears at The text section will echo top left Click on Tyr 322 You clicked 2BIW pdb2 B TYR 322 CG ni Selector selection sele defined with 0 atoms Note if Tyr 322 is still selected In sele acer 2BIW pdb2 B TYR 322 CG may be necessary to click twice The first Selector selection sele defined with 12 atoms click will unselect Tyr 322 and the Mutagenesis 5 rotamers loaded second will select it for mutation A new copy of Tyr322 will be displayed in white and corresponds to an ideal rotation The default is that it is a backbone dependent rotamer Upon selection a slight de zooming may occur Zoom back closer with the right button mouse Top gt Down movement e When NACAR ice r lnal n co am Ib An oro ane m0 61 r al i s 10 0
28. el sele Ligand Note the word in quotes here ligand can be changed to any other word such as my molecule or carotenoid etc To clear the label simply type Label sele Mouse Wizard Help Y TASK Switch the selection mode back to residues 3 Button Viewing Mode 7 5 Greek alphabet Letters from the Greek alphabet can be added to text entered labels The commands call on special fonts called Unicode UTF8 fonts The Greek font is 316 the alpha letter is number 261 and omega is 277 268 and 269 are not used While alpha and beta might be most useful to label a helices and B sheets the rest of the alphabet might be useful to label specialized items V OPTIONAL Label the atom with alpha and beta Greek letters and some text Type the following commands within the text box label sele 3816 261 816 262 Greek Letters lt press enter gt ess e reak Letters set label_size 22 set label_size 40 Or write part of the alphabet Biochem 660 2008 label sele 316 261 316 262 316 263 316 264 316 265 316 266 316 267 316 270 316 271 316 272 316 273 316 274 316 275 316 276 316 277 n A 7 6 More information There are too many aspects to labeling Exhaustive information can be found at http Awww pymolwiki org index php Label OW 8 PyMol Exercise H Saving a PyMol session A session file is a binary file containing all the informati
29. ence manual and is shown both within the text area of the external GUI and within the graphical viewer Press the Esc Key to go back to the graphical view Note PyMol is written with the language Python and some specifics about this is given at the end of the help data Unless noted you do not have to remember these commands se ste Ms Ms 4 PyMol Exercise D Action preset menus This is mostly a self paced exploration of one of the menus that is sure to change over time as PyMol evolves Preliminary If you are not continuing this exercise from the previous exercise do the following tasks y load the structure 2BIW pdb2 as in Exercise B y then click S gt Cartoon to be in a similar sate as in the previous exercise 4 1 Preset menus automated complex imaging The preset menu is part of the Action set of the ASHLC menus controlling the aspect of molecules from the Names Panel Y TASK Follow this menu cascade sequence to return to the default view as when you just opened the molecule No rotation will occurs 2BIW pdb2 gt A gt preset gt default This command has a similar effect but is not the same as the following cascade hide everything and show lines AGES 2BIW pdb2 gt H gt everything nann orient center and origin a lace drag r simple oreset 2BIW pdb2 gt S gt lines le no solvent or Bball and stick align P i b factor putty generate Note the preset opt
30. f your PyMol session the following info is useful to capture the screen or a portion of the screen Macintosh Windows Full screen do Shift 4 Full screen Print Screen key Screen selection Shift 3 Screen selection Shareware 3 11 Ray Tracing images The previous image is rather crude in terms of graphics and resolution PyMol offers an internal ray tracer to create stunning rendered images with a high visual quality much more pleasant to the eye and ideal for publication Y TASK To create a standard ray traced image of the current Viewer scene click the Ray button at the top right of the external GUI Setting Scene Mouse Wizard Help Reset J Zoom J Orient Drav Unpick Deselect J Rock Get NO 1 lt X lt stop Play X gt X gt 1X MClear _Unpick Deselect Rock Gaia i lt lt stop Play gt gt I MClear_ The rendering will take a few seconds to a few minutes depending on the complexity of the PDB file and the chosen display and will also depend on the speed of the computer CPU Once rendered the image appears within the Viewer To save the file use the save cascade as above File gt Save Image SKN Zoomed side by side comparison between the pymol image and the ray traced image note the jagginess of the original image and the smooth appearance of the ray traced image with shadows as a bonus This is useful to create preview images
31. hin the text window You clicked 2BIW pdb2 B TYR 322 CG Therefore we know that Tyrosine 322 is the residue we chose see below for explanation on the nomenclature Now slide the sequence cursor to the right to move the sequence displayed until you find the region of the selected TYR If you have the one letter code engaged it appears under the number 321 However we know it is 322 If you have engaged the three letter code as instructed above TYR 322 is shown highlighted within the sequence line Display the sequence line to see residues PHE 303 and HIS 304 With the mouse click on residue 303 and residue 304 within the sequence line Note that they are selected within the graphical window The arrows within the following image show where you should look As before transform those side chains to a thicker stick with the menu cascade sele gt S gt sticks foe see 206 311 316 321 al WAL HIS ALA ASN ALA PHE GLU GLU ASN GLY LYS ILE ILE LEU ASP SER ILE CYS ASHE E Eis AN MFG Quiz question We just selected amino acids TYR 322 PHE 303 and HIS 304 Can you describe with one word one important quality of this binding pocket Answer This binding pocket has the following quality Biochem 660 2008 V iNFO T l mize lox Clip Movs z A A F ki vS rig Clip Mov The sequence viewer can also be engaged by 7a ent Menu clicking on the S at the bottom right of PyMol Resid where other reminders are shown
32. ions will set some eee yeas variables that are specific to these views Bic ciesc mesa and may change further drawings To ee eee ENE pretty iwi solven remove the effect of these presets BM publication hydrogens remove waters affecting an object representation use SSS lt the A gt preset gt default menu cascade Yy masking reset parameters Puttans e SshFt compute Note to get back to the original opening view simply type reset at the PyMOL gt line command 4 2 Preset Options Exploring more TASK Explore the other menus of this series The cascade menu 2BIW pdb2 gt A gt preset is assumed in the following commands just continue with the suggested command E g for the first one the complete command would be 2BIW pdb2 gt A gt preset gt simple simple The tracing can then be made thicker by unselecting the smooth option with the following menu cascade Setting gt Ribbon gt Smooth Note a set of 3 histidines is also shown Biochem 660 2008 b factor putty The segments with the highest temperature factor are shown as thicker cylinders Regions of better resolution have thinner diameter and are usually found at the core of the protein Mostly loops in Swan the outside of the protein wobble the core aS Za ARC portions of the proteins usually appear more a w9 stable than the external loops This is mostly useful for crystallographers but is a cool representation Color
33. it might work g Desktop on your current system However you will likely find that when you get to the Open entry of the files you want to open are shown in gray and therefore cannot be opened The easy fix is to rename the file from pdb1 or pdb2 to simply pdb before you try to open it The load line command option circumvents all file naming convention issues ste ste Ms Ms lt Overflow Y gt 2BIW pdb im m ar r Biochem 660 2008 3 PyMol Exercise C Understanding the PyMol interface a READ This exercise continues on the previous exercise where 2BIW pdb2 was loaded within the PyMol software Your screen should be similar to this image without the extra markings 6 9 MacPyMOL Reset X Zoom K Draw W Ray b i Rock ye Hide Sele pd Get View View F 2 SYNECHOCYSTIS NATIVE ENZYME TITLE EXTERNAL GU ObjectMolecule Read crystal symmetry T information Symmetry Found 4 symmetry operators CmdLoad 2BIW pdb 2 loaded as 2BIW pdb2 bd PyMOL gt et Jamec HEEB mF Names f zus ng nr Panel INTERNAL VIEWER S Buttona fee amp Reus ae fe eS qove Sli Se E ase 1 Cine wS Ctrl reS Pkire Phil Woe Eiesn Sela Hirie Eia Ma SnelClk 7 Cent Menu ABICTE Menu z PRAt Residues 1 4 perce iste we Viewing PuhMOl gt _ The Viewer and Internal GUI are the parts we will use most The default size of the image in the
34. me the top left Click on the white Tyr 322 A appears at e Click on the No Mutation button and select a new amino acid PHE PyMOL gt lall 2BIW pdb2 H 2BIW pdb2_pol_co C mutation A SA L C a Move Movd Slab x Box Clip Mov PkAt Pki MvS2 2 Orig Clip Moved Cent Menu PRAE acini e Click the grey button Apply e Click the grey button Done Biochem 660 2008 Note Clicking Done will exit the Mutagenesis Wizard Y TASK y Quit PyMol 12 PyMol Exercise L Model Building helix modeling example SY READ PyMol offers modeling options for small molecules and proteins For example you can build an alpha helix from scratch with a specific sequence The builder interface to accomplish this is different depending on the operating system On Windows and X11 Unix Linux versions of PyMol the External GUI has an extra set of buttons to build by clicking on the various components to be assembled such as amino acids The MacPyMol version has the same capability but instead of clicking icons menu items are chosen Windows builder interface nnn Small Chemical molecules builder panel The PyMOL Molecular Graphics System SEE File Edit Build Movie Display Setting Scene Mouse Wizard Plugin Help ae Reset Zoom Orient Draw Ray Chemical Atoms c n 9 2 F cl Unpick Deselect Rock Get view Protein Fragments CH4 C C C C NC 0 C 0N C O S 02 je lt Stop Play gt
35. mesh surface b i You should obtain a centered zoomed view of the ligand shown as a stick model within a partial molecular surface pocket The colors are the scheme of previously chosen colors for example if you tried the technical preset earlier the coloring would likely be like a rainbow oS TASK This quick change will make a much nicer image 2BIW pdb2 gt C gt yellows gt sand Now with the mouse click carefully anywhere on the ligand stick to select it As before you will have a sele name within the Names Panel You can now change the color with the following menu cascade sele gt C gt blues gt slate Of course you can pick your own colors Make sure that there is sufficient contrast between the color of the surface and the color of the ligand If you have not yet done so rotate the molecule to select a nice viewing angle If you want to add a more stunning effect click on the ray button as we did before to complete your publication quality picture Note If you are preparing a figure for a black and white print publication it might be advantageous to use the various gray scales black and white within the grays option wW Biochem 660 2008 5 PyMol Exercise E Sequence Viewer Preliminary We are still working with the 2BIW pdb2 file loaded above Review exercise B if you need to reload the structure This exercise assumes you have just completed creating the above view with the
36. nd essentials and online at http www rcsb org On the left menu table click on Dictionaries amp File Formats and select PDB format In summary PDB files are the simplest plain text files organized in column format in lines of at most 80 characters Each line record starts with a keyword The top of the file header contains informative records while ATOM and HETATM records represent the 3D coordinates Open 2BIW pdb2 with a simple word processor the simpler the better For example TextEdit on a Macintosh or Wordpad in Windows Windows simple Notepad usually does not work because it does not translate end of line characters Scroll up and down the text file and observe the contents Since we only saved a portion of the original PDB data by selecting a biological unit monomer the header is somewhat shorter 428 lines before the first ATOM record than if we had saved the complete PDB file 998 lines you can download the complete 2BIW pdb file if you wish Note that within the 2BIW pdb2 header the XXXX next to the release date on the first line are replacing the 2BIw PDB ID code as 2BIW pdb2 does not represent the complete PDB records Biochem 660 2008 J WwW PHPU J Z HEADER OXIDOREDUCTASE 19 JAN 05 XXXX TITLE CRYSTAL STRUCTURE OF APOCAROTENOID CLEAVAGE OXYGENASE FROM TITLE 2 SYNECHOCYSTIS NATIVE ENZYME COMPND APOCAROTENOID CLEAVING OXYGENASE KEYWDS OXYGENASE NON HEME IRON CAROTENOID CLE
37. on Show Hide Lablel and Color Some menu items have submenu components Selections made under the all line will affect all the opened molecules Rule Once a selection is shown S it must be selectively hidden H as it is not removed when another selection S is made Selections are therefore additive which allows for the creation of complex images with mixed graphical representations 3 5 Cartoon Y TASK Let s first make a cartoon representation of this protein within the 2BIW line v click S and v select Cartoon The molecule is now shown as both cartoon and wireframe Remove the wireframe by clicking H and lines Note that within the S submenu list the as menu contains a lot of redundancies Options most options can be set within the Setting menu within the top menu bar For example it is possible to change the way all alpha helices are rendered Scene Mouse Wizard Help S TASK Edit all r Colors Side Chain Helper Ribbon gt y Round Helices Follow the menu cascade Transparency gt Fancy Helices Rendering mr v Flat Sheets Setting gt Cartoon gt Cylindrical Helices une coum eu Oba E Seals y Auto Show New Selections Discrete Colors y Auto Hide Selections i Select this option again to remove its effect Auto Remove Hydrogens felt ERN and do the following Show Text Hide Text Overlay Text Setting gt Cartoon gt Fancy Helices Testing other cartoon settings Eng
38. on and graphical displays currently within PyMol It is a way to save the current state of the software with all that it contains Later the file can be opened and everything is restored 8 1 Saving the session file 8 2 siiam Edit Build Movie Save Session aS From the top menu follow the menu cascade E File gt Save Session As In the next window enter a name MySession and save the resulting file on the Desktop to easily find it again Save As MySession f Where fs Desktop 4 The susscessful writing of the file will be reported within the text window of the External GUI and a file called Mysession pse on the desktop pse is added automatically MySession pse Now quit PyMol File gt Quit 8 3 Restoring the session file While it is possible to simply double click on the MySession pse icon this could create problems if there are multiple copies of PyMol within your computer and even more so if they are various versions of the software It is therefore best to first open the PyMol software version you want to utilize A TASK For this exercise double click on the Applications gt Classes gt MacPyMol software to open it Within the PyMol top menu follow the menu cascade File gt Open and then select Mysession pse from the Desktop All the PyMol names and selected items are restored as if you had just made them even if days have passed since you saved the file How convenient
39. s gt within selection all A s H G A new objects DENN ala_polar_conts 2BIW pd b2_ polar E ci P _conts is created a eee TH The yellow default ek At Pereiran SS color for the dashed line is easily changed with the C menu for this object For example a darker color can be chosen for display against a white background Note choosing to other atoms in object would show additional hydrogen bonds of the helix side chains to other parts of the protein Note for more complex issues regarding hydrogen bonds or adding hydrogen atoms refer to the web link above OWE PyMol continues with PyMol 2 L02 module Class notes
40. s described HKJ Edit Build Movie above use the menu cascade Open 30 Save Session 5 File gt Save Molecule SERAN Kony Save Imaae Choose obj01 within the Save Molecule panel 9999 Save Molecule Which object or selection would you like to save Choose a file name and save the file e g Name obj01 pdb The file will be a PDB file with only oo the object 3D data and contains HETATM and CONECT records With a word processor open the PDB file and replace HETATM with ATOM _ d TASK Delete the current obj01 with the menu cascade Names Panel obj01 gt A gt delete object Open the PDB file obj01 pdb with PyMol menu cascade File gt Open or use the load line command A new obj01 now appears within the Names Panel and the S gt surface menu is now working for this object a turning off automatic zooming and clipping with new objects When we created object objO1 from sele above the Scene Mouse default action of PyMol was to automatically zoom to the So ee Colors new object in that case the ligand and reduce the clipping Cartoon Ribbon planes That can be annoying in some cases but could Paracas always be reversed with the line command reset or with Rendering the menu Display gt Clip gt None or with the Display gt ignore PDB Segment Ide Zoom menu options v Auto Show New Selecti v Auto Hide Selections This option is turned off by un checking the menu item
41. t the parentheses that becomes independent of the original PDB file SY TASK For example the ligand can be made into a separate entry y Click on the ligand becomes the current sele y Click on the A on the sele line and choose copy to object a new entry called objO1 appears within Names Panel and an automatic Zooming occurs y Click on the S on the obj01 line to change the object appearance e g as Stick Note If you make obj01 invisible by clicking on the objO1 icon the ligand is still visible because it is also part of the 2BIW pdb2 file Note If the option extract object was used instead the ligand would have been removed from the 2BIW pdb2 object and would no longer be available under that name Therefore the 2 options both create a new object one makes a copy of the Original and the other moves it _70 M Biochem 660 2008 10 2 Making a surface for the ligand itself Question Why can t make a surface for the ligand itself Surfaces are reserved for ATOM records only Typically ligands are stored as hetero atom HETATM records but authors of the PDB file may choose otherwise hence always check within the file with a word processor One way to circumvent this is to make the ligand into an independent object see pervious paragraph save it from PyMol into a text file replace the ATOM word with HETATM and reopen the file with PyMol d TASK Assuming you have created obj01 a
42. the object created when opening file 2BIW pdb2 The complete selection contains 12 atoms which make up the complete Tyrosine without the hydrogens since these are usually not present in PDB files Now that the ligand atoms are segregated within the name of sele we can change its color if we want by the following cascade within the Names Panel V TASK sele gt C gt by element gt CHNOS Biochem 660 2008 selecting the first CHNOS after HNOS in the list would display the ligand as green with one red oxygen 3 10 Saving an image If you still see the selection dots over the ligand from the previous section simply click anywhere on the white background to unselect Alternatively click on the Hide Sele button at the top right hand side of the external GUI Y TASK Rotate the molecule to find a perspective that you deem instructive of the conformation of the protein and it s bound ligand Follow this menu cascade to save the image H Edit Build Movie currently within the Viewer Open 0 Save Session 36S Save Session AS o gt File gt Save Save Molecule Image wee BR da A a oo Then replace the default word pymol to give a name to the file you want to save a ere EE Desktop E e g image1 Cancel Save The image will be saved as a PNG image on the desktop vA INFO Screen Capture If for any reason you cannot save the current image o
43. tive Ctrl K Histidine Opt H 7 Cycloh Opt 6 Make pk1 Negative Ctrl J kolca Oi Make pk1 Positive Ctrl K TOONOKY TP Make pk1 Neutral Ctrl U Make pk1 Negative Ctrl J Cycloheptyl Opt 7 Leucine Opt L Fluorine Ctrl F Lysine Opt K Make pk1 Neutral Ctrl U pare nai cast al N Methy Opt Z Methane Phenylalanine Opt F Nitrogen Ctrl N Proline Opt P Oxygen Ctri O Serine Opt S Phenyl Opt 9 Threonine Opt T Sulfur Ctrl S Tryptophan Opt W Sulfonyl Opt 3 Tyrosine Opt Y Phosphorus Ctrl P Valine Opt V Antiparalle Beta Sheet Parallel Beta Sheet SY INFO MacPyMol is a hybrid version that also contains the X11 version To access the X11 version simply copy and rename the MacPyMol application e g on the Desktop with the menu cascade y Click once on MacPyMol y use the Finder menu Edit gt Copy Click anywhere on the Desktop then Edit gt Paste Change the name from MacPyMol Copy to PyMOLX11Hybrid The change of name will activate the X11 version embedded within upon double clicking Note X11 has to be installed on the Macintosh for this to work Current versions of the Mac OS install X11 by default Note an Xterm terminal will appear The X11 version looks very similar to the Windows version including a split between the external and internal GUIs X11 builder nte facea Small Chemical molecules builder panel Biochem 660 2008
44. within the file In the following example we will download one functional biological subunit in this case a monomer e Open a web browser such as Safari or Firefox of TASK e Point your web browser to www rcsb org e Inthe Search box enter the following ID 2biw and click SEARCH button Advanced Search Home search Structure Queries e On the left column click E 2BIW Download Files to show Download Files submenus i e Click the first option PDB File Header Biological UnitCoordinates 2 m mmCIF File E mmCIF gz E mmCIF File Header EL Home search Structure Queries Note DO NOT USE Biological Unit Coordinates 1 ca PDBML XML gz E PDBML XML File Header gt Download Files E PDBML XML File E Structure Factors File e The file is saved on the E PASTA Sequana m Structure Factors gz gt Display Files E Biological Unit Coordinates 1 desktop as 2BIW pdb2 gt Display Molecule E Biological Unit Coordinates 2 E Structural Reports E Biological Unit Coordinates 3 Note The file might be delivered as a gt Structure Analysis poles cette al tage gt Help FASTA Sequence gunzipped gz file However the pega browser should decode it automatically You can now close your browser or hide it Command H Optional exercise explore the text content of the PDB file 2BIW pdb2 You can review details on the PDB file format in the previous section titled Desktop molecular graphics backgrou
45. within this same menu list Biochem 660 2008 Changing the color of the ribbon is easy with the following cascade menu within the PyMol Names Panel of the Internal GUI under the C menu as shown in the following menu cascade Y TASK 2BIW pdb2 gt C gt oranges gt orange You may also choose another option which is to color by secondary structure by following this menu cascade instead 2BIW pdb2 gt C gt by ss gt Helix Sheet Loop choose one of the proposed color options displayed e g red yellow green 3 7 Displaying adding ligand When we opted to show the molecule as a cartoon above one thing happened the protein was shown as the familiar cartoon representation but any ligand such as co enzymes substrates or inhibitors which is the true for this file it simply does not appear as it is not part of the cartoon representation of the protein Here we will rescue the ligand This menu cascade is also within the ASHLC menus of the PyMol Internal GUI Names Panel Since ligands are usually small organic molecules the following cascade within the Show menu for line 2BIW will show the ligand Perform the following cascade Y TASK 2BIW pdb2 gt S gt organic gt spheres This cascade will select the carotenoid present within Sak me the PDB file idisulfides Note that it is the same color as other parts of the protein as it is part of the name 2BIW pdb2 line It will
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