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Contents 1 Balltools User Manual 2 Command line tools

1. 49 55 60 66 82 84 97 A Y Y N 129 PHE 145 VAL A N 159 TYR 162 AS N 171 MET 187 GL U No output file name was given COIL 1 STRAND 7 COIL 10 STRAND 20 COIL 25 HELIX 29 COIL 36 HELIX 40 COIL 48 STRAND 54 COIL 59 HELIX 65 COIL 81 HELIX 83 COIL 96 HELIX 103 COIL 114 HELIX 117 COIL 125 HELIX 127 6 9 19 24 28 35 39 47 53 58 64 80 82 95 10 11 11 12 12 14 2 3 6 4 6 2 YEDGK YTT Q 13 GLU 23 LEU 28 PHE 32 HIS 739 VAL 43 SER 51 PRO 57 THR 762 ASN 68 LEU 84 VAL 86 ASP 99 THR 12 22 27 31 38 42 50 56 61 67 85 98 1 LYS 24 GLU 29 PHE 33 CYS 40 LEU gt 44 ASP gt 52 GLU gt S8 LYS 63 PHE 69 GLY gt 87 LYS 13 23 28 32 39 43 51 57 62 68 86 15 PRO 14 25 PHE 24 30 CYS 34 TYR 33 41 HIS 45 ASN 44 53 GLY 52 59 TYR 58 64 MET 63 70 LYS 69 88 VAL 87 100 GLN 99 101 THR 100 102 ILE 101 103 ARG 102 104 106 SER 105 107 ASP 106 115 117 ILE 116 118 LYS 118 120 GLU 119 121 GLU 120 126 128 SER 128 7130 VAL 129 131 VAL 130 144 146 GLN 145 147 LEU 146 151 7 153 MET 152 154 PHE 153 155 157 GLY 156 158 LYS 158 160 GLN 159 161 L
2. entirety of the molecule Default is doing so h help Ignores every other parameter Print this help message and exit Example disulfideBondMaker if fnameIn pdb of fnameDut pdb u 0 O 1 v 0 1 0 as o add cxxc Please note that o seems to require that hydrogen bonds are added So please refrain from using no_hyd at the same time Also please note that some Phyre produced files already seem to contain Cysteine Bonds If these are met with BALL Hydrogen completion a third bond is opened for the sulfur atoms forming the bridge This is observable if done in BALLView too A workaround for this is including add to the call disulfideBondMaker will then drop the excess hydrogen after the completion step Contact Markus Hermann Koch markus hermann koch rub de October 2013 Here is an example call 1A2L has no disulfide bond The program creates it does a standard energy minimization and moves and turns the result ing molecule in such a way that the sulphur attached carbon of the first cysteine comes into the origin said sulphur S becomes codirectional with u 0 0 1 and the base carbon Co comes into the half plane au Bv where a R 8 R and v 0 1 0 disulfideBondMaker if 1A2L pdb of 1A2L_closed pdb u 0 0 1 v 0 1 O as o add cxxc disulfideBondMaker if 1A2L_closed pdb of 1A2L_closed_corrected pdb u 0 0 1 v O 1 O as o cxxc 10 TODO You may wonder why there are in fact two calls abo
3. ordered list and exits The name conventions as used by BALL h help Print this help message and exit Note that the print function may be very helpful determining valid names and indecies Contact Markus Hermann Koch markus hermann koch rub de August 2013 The example call atomGeometry2csv 1A2M pdb geom csv cxxc res CYS deg leads to a csv describing the geometry of the atoms included within CYS In addition extra lines for the cxxc motif are included and all angles are given in degree A single atom may have more than one line devoted to itself depending on how many bonds of interest to neighbouring atoms it maintains rch pe N Fey es ss owt ose me res E EE E Ne er pe Pas e Sr ell vom ses are oe bonds el x y z a0 el x y 2 dist a0 al el x y z distal dist 0 1 angle tors_angle ss dist 2_ 5 2CYS 29 aSG Sulphur 28 175 61408 84 577CYS S CB Carbon 28 673 62098 86 18 1 81486 CYS S SG Sulphur 29 328 62 445 83 268 2 02035 6 102683 3_ cys 2CYS 132_aSG Sulphur 29 328 62445 83 268CYS S SG Sulphur 28 175 61 408 84 577 2 02935 CYS S CB Carbon 28 318 63 896 82 835 1 82016 304059 104 214 903266 2 02935 4 _ cys 2r29a0 Nitrogen 28 077 63 703 87 912 CYS S CA Carbon 27 549 62 639 87 067 145771PHE C Carbon 27 397 64214 88 933 1 32889 244656 122 731 NA 5_ cys 3 29 1 Carbon 27 549 62639 87 067 CYS S N Nitrogen 28
4. tex Basically it takes a function fg x which is represented by a suitable implementation of Derivator an initial parameter set o as well as data sets x1 n and y1 Yn and a weights n vector w Then it attempts to solve the local extreme value problem by finding a null of V Fo Here 0 91 Vk and V d dvj d dvx The Newton iteration starts at 3 3 Outlook For once the balltools library will be employed in the metagenomics project for optimization of the parameters used for the energy minimiza tion To this end a similarity measure for two proteins will be implemented next On the other hand especially structAlign might offer potential for a pub lication of its own Competition albeit non secondary structure employing may be found here http proteopedia org wiki index php Structural_alignment_tools 16
5. total energy 19635 3 kJ mol iteration 600 RMS gradient 3 64588 kJ mol A total energy 20134 2 kJ mol iteration 700 RMS gradient 3 31071 kJ mol A total energy 20987 2 kJ mol iteration 800 RMS gradient 2 44736 kJ mol A total energy 20881 7 kJ mol iteration 900 RMS gradient 1 85797 kJ mol A total energy 21153 9 kJ mol iteration 1000 RMS gradient 1 6139 kJ mol A total energy 21241 1 kJ mol iteration 1100 RMS gradient 2 10721 kJ mol A total energy 21035 3 kJ mol iteration 1200 RMS gradient 1 20924 kJ mol A total energy 21575 2 kJ mol iteration 1300 RMS gradient 1 67168 kJ mol A total energy 21637 1 kJ mol iteration 1400 RMS gradient 1 92808 kJ mol A total energy 21699 kJ mol iteration 1500 RMS gradient 2 5221 kJ mol A total energy 21992 7 kJ mol iteration 1600 RMS gradient 2 3177 kJ mol A total energy 22414 4 kJ mol iteration 1700 RMS gradient 2 43856 kJ mol A total energy 22419 7 kJ mol iteration 1800 RMS gradient 0 739445 kJ mol A total energy 22918 5 kJ mol iteration 1900 RMS gradient 1 38635 kJ mol A total energy 22839 5 kJ mol Stopping Minimization Final gradient norm 0 443127 kJ mol Ang Aligning System to CYS 0 u 0 000 0 000 1 000 v 0 000 1 000 0 000 2 4 atomGeometry2csv Takes a protein and a list of amino residues atoms or cxxc motifs of interest and produces a csv describing lengths and angles between the associated atoms Due to special interest in the case of cxxc motifs and a closed dis
6. 077 63 703 87912 1 45771CYS S C Carbon 26 348 63 108 86 243 153015 247569 111885 6 CYS 3 29 1 Carbon 27549 62639 87 067CYS S N Nitrogen 28077 63 703 87912 145771 5 5 Carbon 28 673 62098 86 18 1 53063 2 43538 109 143 NA 7_ cys 3 29 1 Carbon 27 549 62639 87 067 CYS S C Carbon 26348 63 108 86 243 153015 5 5 Carbon 28 673 62098 86 18 1 53063 253569 111879 cys 3 29 2 Carbon 26 348 63 108 86 243 CYS S CA Carbon 27 549 62639 87067 153015 5 5 Oxygen 26 477 63955 85 358 1 23177 240868 121029 9 cys 3 29 2 Carbon 26 348 63 108 86 243CYS S CA Carbon 27 549 62639 87 067 1 53015PRO N Nitrogen 25 156 62556 86536 134589 245261 116885 10 CYS 3 29 2 Carbon 26 348 63 108 86 243 CYS S O Oxygen 26 477 63 955 85 358 1 23177 PRO N Nitrogen 25 156 62556 86 536 1 34589 2 25609 122086 NA 11 CYS 1r29a3 Oxygen 26 477 63 955 85 358 CYS S C Carbon 26 348 63 108 86 243 1 23177 NA NA NA NA NA NA NA NA 12 CYS 2r29a4 Carbon _ 28 673 62098 86 18 CYS S SG Sulphur 28 175 61 408 84 577 1 81486 CYS S CA Carbon 27 549 62 630 87 067 1 53063 284734 116 406 NA NA 13 CYS 2r29a5 Sulphur 28 175 61 408 84 577 CYS S CB Carbon 28 673 62098 86 18 1 81486 CYS S SG Sulphur 29 328 62 445 83 268 2 02935 300486 102 683 NA NA 14 CYS 232 0 Nitrogen 26 328 62533 82 498 CYS S CA Carbon 2718 63543 81 889 1 45495 HIS C Carbon 25 295 61 989 81 863 1329 244312 122 637 NA NA 1s _ cYs 332 1 Car
7. EU 161 163 PRO 162 164 GLN 163 170 172 ASP 171 173 VAL 172 186 188 LYS Omitting to write to disk LEKPVAGAPQ VLEFF SFFC PHCYQ EVLH FE ISDNVKKK LPEGV MTKYH VNFMG DLGKDLTQAWAVAMAL GV K G EDKVTVPLFEGVQ KTQTI RS ASDIRDVFINA GIK GEEYDAAW NS FVVKSLVAQQEKAAAD 16 VAL 26 PHE 35 GLN gt 46 VAL 54 VAL 60 HIS 65 GLY gt 71 ASP 89 THR 15 34 45 53 64 70 88 717 ALA 16 18 GLY 36 PHE 35 37 GLU 4T LYS 46 48 LYS 55 LYS 66 GLY 72 LEU 71 73 THR 90 VAL 89 91 PRO 108 ILE 107 109 ARG 108 1107 AS 122 121 27 132 LYS 131 148 ARG 147 155 VAL 165 GLY 164 174 PHE 173 123 ASP 122 124 AL 133 SER 132 13P LE 149 GLY 148 150 VA 166 MET 165 1677 AS 175 VAL 174 176 GL COIL 143 149 VQLRGVP STRAND 150 153 AMFV COIL 154 156 NGK STRAND 157 159 YQL COIL 160 168 NPQGMDTSN HELIX 169 184 MDVFVQQYADTVKYLS COIL 185 186 EK 2 3 disulfideBondMaker In the metagenomics project at our institute we had need of a function that can create or dissolve a disulfide bond within a given cxxc motif This is the primary task of this tool In a nutshell it works in four major steps 1 The site of the cxxc motif of interest is either given by the user or identi
8. Markus Hermann Koch markus hermann koch rub de 27 02 2014 Contents 1 Balltools User Manual 1 1 1 What this is all about 1 2 Command line tools 1 21 cstructAlion 2 0 04 Gerea ae et ei A a E E 2 2 2 Secondary ZSV o eb ee a ke 7 2 3 disulfideBondMaker 9 2 4 atomGeometry2csv 12 25 MOVER sss i oe Ae ET even OO ee a 13 3 C classes 14 3 1 About the Balltools classes 14 DA tye Bild Rice en Goad Sdn Le ied 14 3 1 2 MoleculeHandler 14 3 1 3 DisulfideHandler 14 3 1 4 14 3 2 About the Optimization classes 15 SQ Matra ey eh Sa a es ec ike os 15 Bi 220 Tati ane oe a aa hee Bo Ae 15 3 2 3 ADETIVALOR e est 2A RS hb Se ot Bas Palo 15 3 24 Newtonmiz r we Gate ee i ede Re i 15 3 3 OuUtlOOk ik sae Se Se be ah Ne Oe tt ee A a a 16 1 Balltools User Manual 1 1 What this is all about In the Course of our Metagenomics Project I developed some C programs and two libraries employing the APIs of BALL CBLAS and LAPACKe and offering tools for the modification analysis and structural alignment of ter tiary structure molecules in pdb formatted files This manual presents the balltools command line tools as well as the ballto
9. OIL HELIX COIL YEDGKQ YTT LEKPVAGAPQ VLEFF SFFC PHCYQFE EVLH ISDNVKKK LPEGVK MTKYH VNFMGG DLGKDLTQAWAVAMAL GV EDKVTVPLFEGVQ KTQTIRS ASDIRDVFINA GIK GEEYDAAW NS FVVKSLVAQQEKAAAD VQLRGVP AMFV NGK YQL NPQGMDTSN MDVFVQQYADTVKYLS EK Secondary Structure of Protein 1 COIL STRAND COIL AQYEDGKQ YTT LEKPVAGAPQ 3 STRAND VLEFF 4 COIL SFFC 5 HELIX PHCYQFE 6 COIL EVLH 7 HELIX ISDNV 8 COIL KKKLPEGVK 9 STRAND MTKYH 10 COIL VNFMGG 11 HELIX DLGKDLTQAWAVAMA 12 COIL LGV 13 HELIX EDKVIVPLFEGVQ 14 COIL KTQTIRS 15 HELIX ASDIRDVFINA 16 COIL GIK 17 HELIX GEEYDAAW 18 COIL NS 19 HELIX FVVKSLVAQQEKAAAD 20 COIL VQLRGVP 21 STRAND AMFV 22 COIL NGK 23 STRAND YQL 24 COIL NPQGMDTSN 25 HELIX MDVFVQQYADTVKYLSE 26 COIL K is another example which uses almost every amino residue in the given sequences It was created by the command structAlign 1 0 3TRX pdb if1 1XWC pdb of 3TRX_at_1XWC_by_residues pdb ri 0 104 The example is inspired by this Wikipedia example http en wikipedia org wiki Structural_alignment Alignment of 3TRX to 1XWC from a similar perspective as on said Wikipedia article 2 2 secondary2csv One of the first implemented tools it is heavily inspired by a bit of demo code found on the internet The program uses BALL API functionality to derive the secondary structure of the proteins in a given pdb file and optionally writes the results
10. bon 2718 63543 81 889CYS S N Nitrogen 26328 62533 82498 1 45495CYS S C Carbon 26 391 64 789 81505 152308 246568 111707 16 CYS 332 1 Carbon 2718 63543 81 889CYS S N Nitrogen 26328 62533 82 498 1 45495CYS S CB Carbon 28 318 63 896 82835 152137 243545 109805 NA 17 CYS 332 1 Carbon 2718 63543 81 889CYS S C Carbon 26391 64 789 81505 152398 5 5 Carbon 28 318 63 896 82835 152137 250593 110747 18 CYS 3r32a2 Carbon 26 391 64 789 81 505 CYS S CA Carbon 27 18 63 543 81889 1 52398 CYS S O Oxyd n 26 675 65 409 80 481 1 23029 2 39153 120 148 NA NA 19 CYS 3r32a2 Carbon 26 391 64 789 81 505 CYS S CA Carbon 27 18 63 543 81 889 1 52398 TYR N Nitrogen 25 397 65 148 82 318 1 33338 243704 116 901 NA NA 20 CYS 3132a2 Carbon 26 391 64 789 B1 505CYS S O Oxygen 26 675 65 409 80 481 1 23029 TYR N Nitrogen 25 397 65 148 82 318 1 33338 225299 122 949 NA NA 2i_ cys 1132a3 Oxygen 26 675 65 409 80 481 CYS S C Carbon 26 391 64789 81 505 1 23029 NA NA NA NA NA NA NA 22 CYS 2r32a4 Carbon 28 318 63 896 82 835 CYS S SG Sulphur 29 328 62 445 83 268 1 82016 CYS S CA Carbon 27 18 63 543 81 889 1 52137 2 77869 112 211 NA 23 CYS 2r32a5 Sulphur 29 328 62445 83 268CYS S SG Sulphur 28 175 61 408 84 577 2 02935 CYS S CB Carbon 28 318 63 896 82 835 1 82016 304059 104 214 90 3266 2 02935 Cysteine bond related geometry data 2 5 movePdb A simple tool for moving and turning a complete BALL system Ro
11. comprise of three major classes and one differentiable function interface with implementations for a rotation around an arbitrary axis with optional translation which is used in structAlign 3 2 1 Matrix Most of the functions in CBLAS and LAPACKe are somewhat awkward to use directly Hence I have decided to implement a simple matrix class that will hide things like row or column majority and offer user friendly functions like basic Matrix calculation by overloading the arithmetic operators in an intuitive fashion There is more convenience stuff like a toString or a toOctave function The latter will return a string representation that can directly be pasted into an Octave or MATLAB environment The other classes in the namespace optimization rely on Matrix 3 2 2 LinAlg Offers everyday task functions like singular value decompositions Moore Penrose generalized inverse matrix kernel calculation Gram Schmidt or thogonalization torsion angle generalized cross product calculations rank and determinant 3 2 3 Derivator This is an abstract class which s implementations describe a function fo x R R 0 R which is totally differentiable to the second degree It offers function signa tures to get values from up to the second derivate Such a Derivator can be used as an argument for the Newtonizer class 3 2 4 Newtonizer The math behind the Newtonizer is explained in great detail within rotation0ptimization
12. eometrically describe the six form defining secondary structure elements found in oxidoreductase molecules See rotation0ptimization ps for details 3 1 4 ProteinComparison At the time of writing February 2014 this class is still a vague idea But it will be detailed within the near future Now that the structural alignment of two related proteins works a usable measure for their alikeness d pto pt1 can be implemented This will allow for an evaluation of the qualtity of an energy minimization Consider for instance a molecule with a potential disulfide bond Within pdb org there may be two variations One where the bond is closed and one where it is open Now for instance starting out with the molecule where the bond is open disulfideBondMaker may be used to close the bond and have BALL do an energy optimization given certain paramters Using a metric like the above mentioned d the quality of the optimization can be assessed by comparing the freshly created closed bond molecule to the http www stack nl dimitri doxygen 14 closed bond molecule from pdb org In turn this can be used to improve the parameters for the optimization 3 2 About the Optimization classes All classes and functions are documented in detail within their header files The optimization classes have their own namespace optimization For ma trix and eigen operations as well as singular value decomopsitions they rely on CBLAS and LAPACKe So far they
13. fied automatically 2 The disulfide bond is altered in the desired manner 3 After the alteration BALL and Amber conjugate gradient methods are employed to do an energy minimization on the molecule thus finding the closest stable form for it 4 The whole molecule is moved and turned in a way that will leave the cxxc motif in a defined position and orientation within the coordinate system Thus it becomes easier to compare several molecules using tools like BALLView The console help text reads Syntax disulfideBondMaker if lt fnameIn gt Required Input file name of lt fnameOut gt Output file name Default fnameIn out ai lt index0 gt lt index1 gt Two sequence indexes O starting to the cysteines to be used cxxc Accept only cysteines that have 2 other amino acids between them Overrides ai si lt skipIndex gt Sequence index O starting All amino acids up to but excluding the indexed one are ignored when auto picking cysteines pi lt index gt Protein index Relevant if there is more than 1 protein in the pdb file Defaults to 0 a2b If given the molecule will be aligned to the cystein bridge of interest Else to the first cysteine default u lt u0 gt lt ul gt lt u2 gt First vector for alignment with respect to the first pertinent cysteine Space will be turned thus that u is parallel to S S if a2b is given or parallel to S C else The default 0 0 0 stands for skip thi
14. in protein 1 si O starting idx to sec struct elements to be used from both proteins si0 O starting idx to sec struct elements to be used from protein 0 sil O starting idx to sec struct elements to be used from protein 1 w After the flag there may follow any number of positive floats These will be used as weights for the Newton iteration The nth weight is assigned to the nth support vector pair When in doubt about the correct order give gt printSecondary vl 4 pretend a shot If w is omitted uniform weighting will be used mi 1000 Maximum number of iterations for the Newton optimization g0 0 4 GammaO for the Newton iteration If the program during an iteration finds a parameter gradient x it will modify the parameter list by x g0 csw le 05 The Newton iteration will consider convergence to be achieved if the parameter gradient is shorter than csw for cst consecutive times cst 10 If csw is underpassed cst consecutive times the program will call the Newton iteration converged add_secondary 0 Force the addition of secondary structures using BALL methods If not present and needed this option may be forced by the program gop 4 Gap opening penalty for the optional Needleman Wunsch Prealignment gep 1 Gap extension penalty for the optional Needleman Wunsch Prealignment blosum opt cnw resources blosum62 mat Blosum Matrix File used for the optional Needleman Wunsch Prealignment
15. into a csv file The help text Prints the secondary structures of the proteins within the given pdb file Also generates a csv formatted representation which will be written into the output file if specified or to the console if not Syntax secondary2csv lt fname input pdb gt lt fname output csv gt Example secondary2csv 1A2L pdb Note If in the pdb the Amino Acid ids are not indexed consecutively and beginning with 1 this indexing will be included into the verbose part of the output Hence the example call secondary2csv 1A2L pdb will lead to the output 3http ball trac bioinf uni sb de wiki CodeLibrary ComputeSecondaryStruture Adding Secondary Structures to given System Protein OXIDOREDUCTASE 1 3 TYR 2 4 GLU 3 5 ASP 4 6 GLY 5 7 LYS 6 8 GLN 10 THR 9 11 THR Coil Strand Coil Strand Coil Helix Coil Helix Coil Strand Coil Helix Coil Helix Coil Helix Coil Helix Coil Helix Coil Strand Coil Strand Coil Helix Coil 7 9 TYR 8 10 20 25 29 36 40 48 54 59 65 81 83 96 103 114 117 125 127 143 150 154 157 160 169 185 12 LEU 22 VAL 27 SER 31 PRO 38 GLU 742 ILE gt 50 LEU 56 MET 61 VAL 67 ASP 83 GLY gt 85 GLU 798 LYS 77105 AL 116 GL 119 GL 127 AS 152 AL 156 AS 11 21 26 30 37 41
16. needleman wunsch Example structAlign ifO0 inO pdb if1 in1 pdb of out pdb thioreductase printSecondary rmsd Markus Hermann Koch markus hermann koch rub de February 2014 Here is an example call for two related molecules 1A2LZ and 1A2M structAlign if0 1A2L pdb if1 1A2M pdb of out pdb thioreductase printSecondary printSupport This produces the alignment depicted in the BALLView screenshot 1A2L red and blue both in the background and aligned to 1A2M which is yellow in the foreground In addition the call leads to a text output describing the molecules and support vectors Note the indexing in the secondary structure blocks These indecies can be used for the parameters si The support vector lists have been shortened for this display Support Vectors for Protein 0 56 3806 80 8755 33 4364 61 6937 79 7918 38 5236 57 4531 68 4591 29 5386 50 1681 78 0424 29 3766 Support Vectors for Protein 1 39 8972 62 7294 71 8136 37 0189 63 0338 78 6559 30 2047 58 5241 66 2088 42 236 57 3597 61 2717 Secondary Structure of Protein 0 OMAN OO 10 amp KE COIL STRAND COIL STRAND COIL HELIX COIL HELIX COIL STRAND COIL HELIX COIL HELIX COIL HELIX COIL HELIX COIL HELIX COIL STRAND COIL STRAND C
17. ols and optimization libraries as they exist today At the time of writing both libraries are still in the same archive but there is no real cause for that since the optimization classes are independent of their balltools siblings This will be remedied before long 2 Command line tools All command line tools can be called without parameters This will cause them to print a verbose help text explaining the available parameters and output http www pdb org 2 1 structAlign Picks a proteinO and a protein1 and aligns the former to the latter one The mathematical how to is described in rotationOptimization tex In a nutshell it does its work in three major steps 1 For each protein a set of weighted support vectors is determined So far this can depend on certain secondary structure elements the cys teine atoms in cxxc motifs or on a preliminary 2D Needleman Wunsch alignment The program will throw an error if the support vector sets are incompatible If you intent to use the parameters si con sider doing some pre alignment analysis using printSecondary and pretend 2 A preoptimization is done First both molecules are translated such that their centers of gravity meet in the coordinate origin Then for each pair of corresponding support vectors there exists a hyperplane of possible axes for a rotation that will given the appropriate angle turn one vector in such a way that it will be codirectional with the other Usually
18. omitNewton 0 If set the Newton iteration will be omitted In that case only the purely algebraic preoptimization will take place printSecondary 0 If given the secondary structure keys for the proteins are printed This may be of interest when deciding on ri and si The amount of detail presented may be customized using the verbosity parameter vl printSupport 0 If given support vector sets for the proteins are calculated and printed This may be of interest when deciding on parameter w evalDiff 0 If given the weighted least squares sum of differences between the support vector sets before and after the alignment will be calculated and printed rmsd The residual root mean square positional deviation as described in Hasegawa Holm Advances and pitfalls of protein structural alignment after pairing via Needleman Wunsch alignment Combined with pretend this will return the rmsd for the unmodified proteins pretend 0 If given no alignment will be done and no output file will be generated Useful in tandem with printSupport and printSecondary vl 3 Verbosity level Ranges in 0 Silence 1 Error 2 Warning 3 Normal 4 Verbose help h Print this help message The program will return EXIT_FAILURE when the support vector sets are obviously incompatible If on at least ERROR verbosity 1 the program will also send some text to STDERR If no support vector information is given the program will try to use
19. rom 1403 atoms Adding missing hydrogens and bonds Found a CxxC motif at indecies 27 and 30 Adding Secondary Structures to given System Deleting Hydrogen using selection code name HG Deleting Hydrogen using selection code name HG Succeeded to build bond Optimizing for maxIt 20000 iterations and maxGrad 0 5 kJ mol A Creating Amber Force Field cannot find stretch parameters for atom types SH SH atoms are CYS30 SG CYS33 SG 11 AmberBend setup cannot find bend parameters for atom types CT SH SH atoms are CYS30 CB C AmberBend setup cannot find bend parameters for atom types CT SH SH atoms are CYS33 CB C AmberTorsion setup cannot find torsion parameter for CT SH SH CT atoms are CYS CB CYS SG Creating Conjugate Gradient Minimzer Setting up ConjugateGradientMinimizer Options MAXIMAL_NUMBER_OF_ITERATIONS gt 20000 ENERGY _OUTPUT_FREQUENCY gt 100 ENERGY_DIFFERENCE_BOUND gt 0 000100 MAX_SAME_ENERGY gt 50 MAX_GRADIENT gt 0 500000 Given options set for Conjugate Gradient Minimizer checked and valid iteration 0 RMS gradient 138 603 kJ mol A total energy 52037 7 kJ mol iteration 100 RMS gradient 24 6961 kJ mol A total energy 3127 38 kJ mol iteration 200 RMS gradient 11 4432 kJ mol A total energy 14195 kJ mol iteration 300 RMS gradient 8 4953 kJ mol A total energy 17555 7 kJ mol iteration 400 RMS gradient 5 26606 kJ mol A total energy 18581 2 kJ mol iteration 500 RMS gradient 6 09872 kJ mol A
20. s feature The molecule will also be translated thus that the second atom in S S or S C is moved to 0 0 0 v lt v0 gt lt 1 gt lt v2 gt Second vector This will only have an effect if u is defined 4Cysteine Wildcard Wildcard Cysteine and linear independent to v After the u action space will be turned around u until S C if a2b or until C CO is within the half plane that is spanned by alpha u beta v where beta gt 0 and alpha in R mv lt w0 w1 w2 gt After the possible axis alignment triggered by u and v the molecule may be translated by this vector as Add secondary Structure o If given a post bridge modificational gradient optimization will be done Space transformations are postponed until after this optimization mi lt max iterations gt Stop optimization after this many iterations Auto includes o Default value is 20000 mg lt max gradient norm gt Maximum gradient norm for an optimization Includes o defaults to 0 5 kJ mol A add Create a disulfide bridge if none is present Auto Drop excess hydrogen atoms in that case rm Remove a disulfide bridge if one is found no_hc No hydrogen correction Per default if a disulfide bridge is buildt or destroyed hydrogen is added or removed from the respective sulphur atoms as appropriate If this for some reason is undesired this parameter leads to skipping hydrogen correction no_hyd Do not add missing hydrogens and bonds to the
21. tates a system around a given axis then translates it Syntax movePdb lt input pdb gt lt output pdb gt lt dx gt lt dy gt lt dz gt rx ry rz angle dx dy dz as used in pdb ATOM coordinates in Angstrom rx ry rz angle If one is given all are needed Rotation axis and angle Angle in degrees 13 3 C classes 3 1 About the Balltools classes All classes and functions are documented in detail within their header files This document only intends to give a general overview As it is it is still a TODO to provide a proper Doxygen documentation as was recommended by Julian Only the most important classes will be described here 3 1 1 Io A tool class offering functionality for loading and saving pdb files printing messages to streams and parsing command line parameters for the diverse balltools 3 1 2 MoleculeHandler A large class for general Molecule modification and analysis It uses many basic BALL functions as well as my own optimization library It offers methods for handling and geometrically measuring secondary structure it erating through molecules molecule specific geometric analysis molecule translation and rotation molecule structural alignment bond and hydrogen addition and BALL Amber energy optimization 3 1 3 DisulfideHandler DisulfideHandler extends MoleculeHandler by methods that are needed to find and modify cxxc cysteine motifs Additionally it also offers methods to find and g
22. there are many such pairs from which an overexpressed LES of normal vectors to said hyperplanes can be derived This LES describes a constrained solution vectors have length 1 minimization problem leading to the optimal axis for the above mentioned prior translation This set of translation 3 angle 1 and axis 2 builds the six starting parameters 09 for the Newton optimization 3 A Newton minimization is done over the six parameters describing translation and rotation of proteino Does a structural alignment of Protein 0 to protein 1 Syntax structAlign ifO lt inFnameO gt if1 lt inFname1 gt inFnameO of lt outFname gt out pdb if0 The input pdb file name for the pdb containing Protein 0 This will be the Protein which will be aligned to Protein 1 if1 lt inFnameO gt Input pdb file name for the pdb containing Protein 1 This will be the Protein to which Protein 0 will be aligned to If omitted both proteins will be taken from inFnameO of out pdb Output pdb for the aligned pto include_pti 0 If set to 1 the Protein 1 will also be included within the output pdb p0 0 Index of Protein 0 in lt inFnameO gt p1 0 Index of Protein 1 in lt inFname1 gt If inFnamel was not given this default value is raised to 1 ch O starting index of relevant chains in Protein 0 and protein 1 If omitted everything will be used the tag may be followed up by any number of indecies ch0 Cumulative speciali
23. ulfide bond the torsion angle of the sulphur attached carbon atoms around the S S axis defined by the disulfide bond is also included Syntax atomGeometry2csv lt fnameIn gt lt fnameOut fnameIn csv gt lt fnameIn gt Required Input file name lt fnameOut gt Output file name Default fnameIn csv pi lt index gt Protein index Relevant if there are more than 1 protein in the pdb file Defaults to 1 standing for every protein in the system cxxc Special interest parameter Include cysteine bonds from cxxc motifs only for those torsion angles will be determined res lt residue name gt Include all atoms found in residues of this kind res may be given as parameter several times Residue names need to be given in 12 uppercase 3 letter codes atom lt atom name gt Include output to atoms of this name atom may be included several times in the parameter list Output will include the atoms of the given name Atom names need to be given in BALL format like CYS SG SG or Sulphur The first in this list is the so called FullName which is not found in BALLView resIndex lt residueIndex gt A specific O starting index to a complete residue of interest atomIndex lt atomIndex gt A specific O starting protein wide index to an atom of iterest deg If given angles are given in degree rather than in rad print For convenience Prints the atoms and residues from the proteins as an
24. ve when the text mentions only one This is to be contributed to a bug that causes the disulfide bond length to receive an unrealistic length if closed and then opti mized directly I have reason to believe this is due to some BALL internal reindexing which is done if an amino residue is altered e g by closing a cysteine bond which hinders Amber to calculate certain values correctly you may notice the AmberBend setup errors within the output below So far my only workaround for this is applying the tool in two consecutive steps e Load the pdb gt Alter the cysteine bond Save the pdb e Load the pdb Energy optimization Do translation and rotation Save the pdb The mentioned TODO is to at least include this workaround into a single call to disulfideBondMaker and to ultimately remove this paragraph A second call merely moves 1A2L in the way described above but skips both the alteration of the disulfide bond and the subsequent optimization disulfideBondMaker if 1A2L pdb of 1A2L_moved pdb u 0 O 1 v 010 as The graphical representation shows a superposition of the coordinate system and the output of both molecules at the sites of the cxxc motif in question Cysteine bond in open and closed state oriented to both carbons and the sulphur atom within the N terminal sided cysteine residue Here is the output of the first call Read PDB 186 fragments found from 1403 atoms Read PDB 186 fragments found f
25. zed version of ch with a focus on pto chi Cumulative specialized version of ch with a focus on ptl cxxc 0 Special interest out of the because we can department really Anyways if added the positions of the three main atoms of the cysteines of each cxxc motif are added to the set of support vectors needleman wunsch nw 0 Build support vector set based on Needleman Wunsch alignment To this end a Needleman Wunsch Alignment is done and the centers of gravity of aligned amino acids will be used as paired support vectors The sets of relevant residues may be restricted using parameters ri thioreductase 0 Adds to other support vector determination parameters If given the six thioreductase form giving secondary structure elements of the proteins will be used for alignment complete_secondary 0 If given it is attempted to use the complete set of secondary structures within the target protein ri O starting index to residues of interest within both proteins If combined with needleman wunsch the parameters ri define areas of interest the Needleman Wunsch alignment will be restricted to Support vectors will be taken from the residues centers of mass For convenience constructs of the form 11 15 for 11 12 13 14 15 are allowed The same holds true for ch ch0 chi si 510 sil riO and ril ri0 O starting idx to residues of interest in protein 0 ril O starting idx to residues of interest

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