Opened 4 years ago
Closed 4 years ago
#5096 closed defect (can't reproduce)
Bad sequence association
Reported by: | Elaine Meng | Owned by: | Eric Pettersen |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Sequence | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.3.dev202108221453 (2021-08-22 14:53:54 UTC) Description tried command "close session" after running modeller Log: > open /Users/meng/Desktop/startup.cxc > alias reset view orient; view initial > alias start tool show $1 > alias whereprefs info path user unversioned config > alias captut open help:user/tutorials/binding-sites.html#cap-example > alias previewts toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu;toolshed reload available > alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload > available > alias btut open > https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding- > sites.html > alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation- > coloring/conservation-coloring.html executed startup.cxc UCSF ChimeraX version: 1.3.dev202108221453 (2021-08-22) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1www format mmcif fromDatabase pdb 1www title: NGF In complex with domain 5 of the TRKA receptor [more info...] Chain information for 1www #1 --- Chain | Description | UniProt V W | protein (nerve growth factor) | NGF_HUMAN X Y | protein (TRKA receptor) | NTRK1_HUMAN > sequence chain /V Alignment identifier is 1/V > refine 1/V:1:10-16 adjacent 0 Unknown command: modeller refine 1/V:1:10-16 adjacent 0 > modeller loops 1/V:1:10-16 adjacentFlexible 0 Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service Opal job id: appModeller9v8Service1629753190510231442370 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appModeller9v8Service1629753190510231442370 stdout.txt = standard output stderr.txt = standard error Modeller job ID appModeller9v8Service1629753190510231442370 finished Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1www, chain V (#1) with chain_V, chain (blank) (#), sequence alignment score = 613.5 RMSD between 104 pruned atom pairs is 0.107 angstroms; (across all 108 pairs: 0.600) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1www, chain V (#1) with chain_V, chain (blank) (#), sequence alignment score = 606.3 RMSD between 104 pruned atom pairs is 0.162 angstroms; (across all 108 pairs: 1.596) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1www, chain V (#1) with chain_V, chain (blank) (#), sequence alignment score = 606.3 RMSD between 103 pruned atom pairs is 0.170 angstroms; (across all 108 pairs: 1.861) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1www, chain V (#1) with chain_V, chain (blank) (#), sequence alignment score = 613.5 RMSD between 105 pruned atom pairs is 0.182 angstroms; (across all 108 pairs: 1.354) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1www, chain V (#1) with chain_V, chain (blank) (#), sequence alignment score = 606.3 RMSD between 104 pruned atom pairs is 0.209 angstroms; (across all 108 pairs: 1.346) Chain information for chain_V --- Chain | Description 2.1/? 2.2/? 2.3/? 2.4/? 2.5/? | No description available > close #2 > modeller loops 1/V:1:all adjacentFlexible 4 numModels 3 Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service Opal job id: appModeller9v8Service1629753282567-324821795 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appModeller9v8Service1629753282567-324821795 stdout.txt = standard output stderr.txt = standard error Modeller job ID appModeller9v8Service1629753282567-324821795 finished Modeller error output Traceback (most recent call last): File "/usr/local/opal-local/bin/modeller9v8.py", line 422, in <module> main() File "/usr/local/opal-local/bin/modeller9v8.py", line 24, in main VersionMap[cf["version"]](cf) File "/usr/local/opal-local/bin/modeller9v8.py", line 39, in v3_run execfile(fn) File "ModellerModelling.py", line 90, in <module> a.make() File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 37, in make automodel.make(self, exit_stage) File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py", line 143, in make atmsel = self._check_select_atoms() File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py", line 679, in _check_select_atoms atmsel = self.select_atoms() File "ModellerModelling.py", line 40, in select_atoms self.residue_range(112, 120) File "/usr/lib64/python2.7/site-packages/modeller/coordinates.py", line 330, in residue_range end = self.residues[end]._num File "/usr/lib64/python2.7/site-packages/modeller/coordinates.py", line 259, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib64/python2.7/site-packages/modeller/util/modutil.py", line 12, in handle_seq_indx raise IndexError("list index out of range") IndexError: list index out of range Modeller run output MODELLER 9.22, 2019/06/19, r11413 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2019 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu 3.10.0-1160.36.2.el7.x86_64 x86_64 Date and time of compilation : 2019/06/19 14:00:54 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2021/08/23 14:14:42 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v22}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v22}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183 openf___224_> Open ${MODINSTALL9v22}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v22}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL9v22}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v22}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v22}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v22}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v22}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v22}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269985 263.657 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 285077 278.396 0.272 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 300477 293.435 0.287 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 331277 323.513 0.316 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 392877 383.669 0.375 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 516077 503.981 0.492 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516105 504.009 0.492 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516133 504.036 0.492 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516161 504.063 0.492 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516189 504.091 0.492 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 517861 505.724 0.494 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 518337 506.188 0.494 Read the alignment from file : alignment.ali Total number of alignment positions: 431 # Code #_Res #_Segm PDB_code Name \------------------------------------------------------------------------------- 1 1www_1 419 4 1www_1 2 chain_V 120 1 chain_V check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ./1www_1.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 645762 630.627 0.616 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 645762 630.627 0.616 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 645933 630.794 0.616 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 646783 631.624 0.617 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 648041 632.853 0.618 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 649945 634.712 0.620 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 649945 634.712 0.620 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 650035 634.800 0.620 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 652891 637.589 0.623 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 652891 637.589 0.623 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 653026 637.721 0.623 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 657310 641.904 0.627 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 657310 641.904 0.627 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 657508 642.098 0.627 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 663934 648.373 0.633 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 663934 648.373 0.633 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 664231 648.663 0.633 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 673853 658.060 0.643 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 673853 658.060 0.643 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 674303 658.499 0.643 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 688753 672.610 0.657 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 688753 672.610 0.657 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 688753 672.610 0.657 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 688753 672.610 0.657 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 689428 673.270 0.657 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 711086 694.420 0.678 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 711086 694.420 0.678 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 712094 695.404 0.679 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 744598 727.146 0.710 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 744598 727.146 0.710 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 746110 728.623 0.712 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 794866 776.236 0.758 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 794092 775.480 0.757 check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST \---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 933344 911.469 0.890 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 934944 913.031 0.892 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 938924 916.918 0.895 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 940924 918.871 0.897 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 943924 921.801 0.900 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 948424 926.195 0.904 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 953996 931.637 0.910 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 956796 934.371 0.912 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 960996 938.473 0.916 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 967296 944.625 0.922 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 970068 947.332 0.925 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 971468 948.699 0.926 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 990151 966.944 0.944 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1084623 1059.202 1.034 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1098815 1073.062 1.048 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 120 945 966 0 0 404 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1139343 1112.640 1.087 patch_______> segment topology patched using RTF: 1 ; SER ; NTER segments residues atoms bonds angles dihedrals impropers: 1 120 945 966 1305 1556 404 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1183839 1156.093 1.129 patch_______> segment topology patched using RTF: 120 ; ALA ; CTER segments residues atoms bonds angles dihedrals impropers: 1 120 946 967 1307 1558 405 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 120 946 967 1307 1558 405 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1193491 1165.519 1.138 patch_______> segment topology patched using RTF: 15 80 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 120 946 968 1309 1561 405 patch_______> segment topology patched using RTF: 58 108 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 120 946 969 1311 1564 405 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1193739 1165.761 1.138 patch_______> segment topology patched using RTF: 68 110 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 120 946 970 1313 1567 405 patch_s_522_> Number of disulfides patched in MODEL: 3 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 857 89 openf___224_> Open chain_V.ini wrpdb___568_> Residues, atoms, selected atoms: 120 946 946 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1300788 1270.301 1.241 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1308980 1278.301 1.248 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1325364 1294.301 1.264 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1358132 1326.301 1.295 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1390900 1358.301 1.326 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1456436 1422.301 1.389 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1489204 1454.301 1.420 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1521972 1486.301 1.451 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1587508 1550.301 1.514 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 970 1313 1480 402 Total number of restraints before, now : 0 4165 make_re_422_> Number of previous, current restraints : 0 4165 make_re_423_> Number of previous, current selected restraints: 0 4165 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656187 1617.370 1.579 openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4165 4283 make_re_423_> Number of previous, current selected restraints: 4165 4283 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386 1.579 openf___224_> Open ${MODINSTALL9v22}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v22}/modlib/omega.mdt getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 122 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 4283 4402 make_re_423_> Number of previous, current selected restraints: 4283 4280 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386 1.579 openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v22}/modlib/chi1.mdt getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4402 4508 make_re_423_> Number of previous, current selected restraints: 4280 4386 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386 1.579 openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v22}/modlib/chi2.mdt getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1721739 1681.386 1.642 make_re_422_> Number of previous, current restraints : 4508 4574 make_re_423_> Number of previous, current selected restraints: 4386 4452 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1721739 1681.386 1.642 openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v22}/modlib/chi3.mdt getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4574 4602 make_re_423_> Number of previous, current selected restraints: 4452 4480 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1721739 1681.386 1.642 openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v22}/modlib/chi4.mdt mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4602 4619 make_re_423_> Number of previous, current selected restraints: 4480 4497 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1994151 1947.413 1.902 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2125223 2075.413 2.027 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2190759 2139.413 2.089 make_re_422_> Number of previous, current restraints : 4619 5995 make_re_423_> Number of previous, current selected restraints: 4497 5873 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 5995 7622 make_re_423_> Number of previous, current selected restraints: 5873 7500 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2321831 2267.413 2.214 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2583975 2523.413 2.464 make_re_422_> Number of previous, current restraints : 7622 9530 make_re_423_> Number of previous, current selected restraints: 7500 9408 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 9530 10276 make_re_423_> Number of previous, current selected restraints: 9408 10154 0 atoms in HETATM/BLK residues constrained to protein atoms within 2.30 angstroms and protein CA atoms within 10.00 angstroms make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 10276 10276 make_re_423_> Number of previous, current selected restraints: 10154 10154 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 10276 10276 make_re_423_> Number of previous, current selected restraints: 10154 10154 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 10276 10276 make_re_423_> Number of previous, current selected restraints: 10154 10154 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 10276 10276 make_re_423_> Number of previous, current selected restraints: 10154 10154 0 atoms in residues without defined topology constrained to be rigid bodies make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 10276 10276 make_re_423_> Number of previous, current selected restraints: 10154 10154 rmdupl__427_> 710 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 10276 9444 openf___224_> Open chain_V.rsr openf___224_> Open chain_V.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2246420 2193.770 2.142 rdcsr2__307_> Number of restraints read : 9444 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 9444 9444 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 No output models from Modeller; see log for Modeller text output. > modeller loops 1/V:1:internal adjacent 4 num 3 Missing or invalid "targets" argument: Sequence position is not a comma- separated list of integer positions or position ranges > modeller loops 1/V:1:non adjacentFlexible 4 numModels 3 Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service Opal job id: appModeller9v8Service16297533412211397169005 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appModeller9v8Service16297533412211397169005 stdout.txt = standard output stderr.txt = standard error Modeller job ID appModeller9v8Service16297533412211397169005 finished Modeller error output Traceback (most recent call last): File "/usr/local/opal-local/bin/modeller9v8.py", line 422, in <module> main() File "/usr/local/opal-local/bin/modeller9v8.py", line 24, in main VersionMap[cf["version"]](cf) File "/usr/local/opal-local/bin/modeller9v8.py", line 39, in v3_run execfile(fn) File "ModellerModelling.py", line 88, in <module> a.make() File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 37, in make automodel.make(self, exit_stage) File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py", line 143, in make atmsel = self._check_select_atoms() File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py", line 679, in _check_select_atoms atmsel = self.select_atoms() File "ModellerModelling.py", line 39, in select_atoms self.residue_range(112, 120) File "/usr/lib64/python2.7/site-packages/modeller/coordinates.py", line 330, in residue_range end = self.residues[end]._num File "/usr/lib64/python2.7/site-packages/modeller/coordinates.py", line 259, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib64/python2.7/site-packages/modeller/util/modutil.py", line 12, in handle_seq_indx raise IndexError("list index out of range") IndexError: list index out of range Modeller run output MODELLER 9.22, 2019/06/19, r11413 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2019 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu 3.10.0-1160.36.2.el7.x86_64 x86_64 Date and time of compilation : 2019/06/19 14:00:54 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2021/08/23 14:15:41 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v22}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v22}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183 openf___224_> Open ${MODINSTALL9v22}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v22}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL9v22}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v22}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v22}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v22}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v22}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v22}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269985 263.657 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 285077 278.396 0.272 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 300477 293.435 0.287 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 331277 323.513 0.316 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 392877 383.669 0.375 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 516077 503.981 0.492 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516105 504.009 0.492 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516133 504.036 0.492 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516161 504.063 0.492 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 516189 504.091 0.492 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 517861 505.724 0.494 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 518337 506.188 0.494 Read the alignment from file : alignment.ali Total number of alignment positions: 431 # Code #_Res #_Segm PDB_code Name \------------------------------------------------------------------------------- 1 1www_1 419 4 1www_1 2 chain_V 120 1 chain_V check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ./1www_1.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 645762 630.627 0.616 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 645762 630.627 0.616 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 645933 630.794 0.616 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 646783 631.624 0.617 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 648041 632.853 0.618 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 649945 634.712 0.620 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 649945 634.712 0.620 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 650035 634.800 0.620 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 652891 637.589 0.623 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 652891 637.589 0.623 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 653026 637.721 0.623 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 657310 641.904 0.627 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 657310 641.904 0.627 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 657508 642.098 0.627 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 663934 648.373 0.633 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 663934 648.373 0.633 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 664231 648.663 0.633 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 673853 658.060 0.643 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 673853 658.060 0.643 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 674303 658.499 0.643 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 688753 672.610 0.657 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 688753 672.610 0.657 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 688753 672.610 0.657 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 688753 672.610 0.657 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 689428 673.270 0.657 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 711086 694.420 0.678 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 711086 694.420 0.678 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 712094 695.404 0.679 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 744598 727.146 0.710 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 744598 727.146 0.710 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 746110 728.623 0.712 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 794866 776.236 0.758 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 794092 775.480 0.757 check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST \---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 933344 911.469 0.890 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 934944 913.031 0.892 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 938924 916.918 0.895 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 940924 918.871 0.897 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 943924 921.801 0.900 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 948424 926.195 0.904 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 953996 931.637 0.910 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 956796 934.371 0.912 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 960996 938.473 0.916 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 967296 944.625 0.922 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 970068 947.332 0.925 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 971468 948.699 0.926 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 990151 966.944 0.944 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1084623 1059.202 1.034 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1098815 1073.062 1.048 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 120 945 966 0 0 404 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1139343 1112.640 1.087 patch_______> segment topology patched using RTF: 1 ; SER ; NTER segments residues atoms bonds angles dihedrals impropers: 1 120 945 966 1305 1556 404 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1183839 1156.093 1.129 patch_______> segment topology patched using RTF: 120 ; ALA ; CTER segments residues atoms bonds angles dihedrals impropers: 1 120 946 967 1307 1558 405 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 120 946 967 1307 1558 405 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1193491 1165.519 1.138 patch_______> segment topology patched using RTF: 15 80 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 120 946 968 1309 1561 405 patch_______> segment topology patched using RTF: 58 108 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 120 946 969 1311 1564 405 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1193739 1165.761 1.138 patch_______> segment topology patched using RTF: 68 110 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 120 946 970 1313 1567 405 patch_s_522_> Number of disulfides patched in MODEL: 3 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 857 89 openf___224_> Open chain_V.ini wrpdb___568_> Residues, atoms, selected atoms: 120 946 946 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1300788 1270.301 1.241 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1308980 1278.301 1.248 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1325364 1294.301 1.264 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1358132 1326.301 1.295 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1390900 1358.301 1.326 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1456436 1422.301 1.389 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1489204 1454.301 1.420 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1521972 1486.301 1.451 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1587508 1550.301 1.514 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 970 1313 1480 402 Total number of restraints before, now : 0 4165 make_re_422_> Number of previous, current restraints : 0 4165 make_re_423_> Number of previous, current selected restraints: 0 4165 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656187 1617.370 1.579 openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v22}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4165 4283 make_re_423_> Number of previous, current selected restraints: 4165 4283 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386 1.579 openf___224_> Open ${MODINSTALL9v22}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v22}/modlib/omega.mdt getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 122 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 4283 4402 make_re_423_> Number of previous, current selected restraints: 4283 4280 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386 1.579 openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v22}/modlib/chi1.mdt getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4402 4508 make_re_423_> Number of previous, current selected restraints: 4280 4386 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1656203 1617.386 1.579 openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v22}/modlib/chi2.mdt getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1721739 1681.386 1.642 make_re_422_> Number of previous, current restraints : 4508 4574 make_re_423_> Number of previous, current selected restraints: 4386 4452 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1721739 1681.386 1.642 openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v22}/modlib/chi3.mdt getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4574 4602 make_re_423_> Number of previous, current selected restraints: 4452 4480 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1721739 1681.386 1.642 openf___224_> Open ${MODINSTALL9v22}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v22}/modlib/chi4.mdt mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 1www_1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 4602 4619 make_re_423_> Number of previous, current selected restraints: 4480 4497 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1994151 1947.413 1.902 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2125223 2075.413 2.027 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2190759 2139.413 2.089 make_re_422_> Number of previous, current restraints : 4619 5995 make_re_423_> Number of previous, current selected restraints: 4497 5873 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 5995 7622 make_re_423_> Number of previous, current selected restraints: 5873 7500 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2321831 2267.413 2.214 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2583975 2523.413 2.464 make_re_422_> Number of previous, current restraints : 7622 9530 make_re_423_> Number of previous, current selected restraints: 7500 9408 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 9530 10276 make_re_423_> Number of previous, current selected restraints: 9408 10154 0 atoms in HETATM/BLK residues constrained to protein atoms within 2.30 angstroms and protein CA atoms within 10.00 angstroms make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 10276 10276 make_re_423_> Number of previous, current selected restraints: 10154 10154 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 10276 10276 make_re_423_> Number of previous, current selected restraints: 10154 10154 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 10276 10276 make_re_423_> Number of previous, current selected restraints: 10154 10154 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 10276 10276 make_re_423_> Number of previous, current selected restraints: 10154 10154 0 atoms in residues without defined topology constrained to be rigid bodies make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 10276 10276 make_re_423_> Number of previous, current selected restraints: 10154 10154 rmdupl__427_> 710 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 10276 9444 openf___224_> Open chain_V.rsr openf___224_> Open chain_V.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2246420 2193.770 2.142 rdcsr2__307_> Number of restraints read : 9444 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 9444 9444 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 No output models from Modeller; see log for Modeller text output. > close > open 2mnr 2mnr title: Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase At 2.5 angstroms resolution: identification of the active site and possible catalytic residues [more info...] Chain information for 2mnr #1 --- Chain | Description | UniProt A | mandelate racemase | MANR_PSEPU Non-standard residues in 2mnr #1 --- MN — manganese (II) ion SO4 — sulfate ion 2mnr mmCIF Assemblies --- 1| author_and_software_defined_assembly > close > open 1muc 1muc title: Structure of muconate lactonizing enzyme At 1.85 angstroms resolution [more info...] Chain information for 1muc #1 --- Chain | Description | UniProt A B | muconate lactonizing enzyme | CATB_PSEPU Non-standard residues in 1muc #1 --- MN — manganese (II) ion 1muc mmCIF Assemblies --- 1| author_and_software_defined_assembly > delete /A > sequence chain /B Alignment identifier is 1/B > select clear > close > open 1gcn 1gcn title: X-ray analysis of glucagon and its relationship to receptor binding [more info...] Chain information for 1gcn #1 --- Chain | Description | UniProt A | glucagon | GLUC_PIG > delete :16-20 > sequence chain /A Alignment identifier is 1/A > modeller loops 1/A:1:all adjacentFlexible 4 numModels 3 Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service Opal job id: appModeller9v8Service1629753992889-221087584 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appModeller9v8Service1629753992889-221087584 stdout.txt = standard output stderr.txt = standard error > ui tool show Log Modeller job ID appModeller9v8Service1629753992889-221087584 finished Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence alignment score = 132.1 RMSD between 18 pruned atom pairs is 0.171 angstroms; (across all 24 pairs: 4.125) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence alignment score = 132.1 RMSD between 18 pruned atom pairs is 0.145 angstroms; (across all 24 pairs: 4.516) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence alignment score = 132.1 RMSD between 19 pruned atom pairs is 0.424 angstroms; (across all 24 pairs: 3.854) Chain information for chain_A --- Chain | Description 2.1/? 2.2/? 2.3/? | No description available > close #2 > modeller loops 1/A:1:all adjacentFlexible 1 numModels 3 Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service Opal job id: appModeller9v8Service16297540519661264090585 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appModeller9v8Service16297540519661264090585 stdout.txt = standard output stderr.txt = standard error Modeller job ID appModeller9v8Service16297540519661264090585 finished Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence alignment score = 133.9 RMSD between 24 pruned atom pairs is 0.141 angstroms; (across all 24 pairs: 0.141) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence alignment score = 123.1 RMSD between 23 pruned atom pairs is 0.037 angstroms; (across all 24 pairs: 1.448) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1gcn, chain A (#1) with chain_A, chain (blank) (#), sequence alignment score = 123.1 RMSD between 23 pruned atom pairs is 0.081 angstroms; (across all 24 pairs: 1.456) Chain information for chain_A --- Chain | Description 2.1/? 2.2/? 2.3/? | No description available > close session Traceback (most recent call last): File "/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 134, in invoke return self._func(self._name, data) File "/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/seqalign/alignment.py", line 635, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) KeyError: <chimerax.atomic.molobject.StructureSeq object at 0x7ffe98811670> Error processing trigger "modified": KeyError: File "/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/seqalign/alignment.py", line 635, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.7.18 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro11,4 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 427.140.8.0.0 SMC Version (system): 2.29f24 Software: System Software Overview: System Version: macOS 10.15.7 (19H1323) Kernel Version: Darwin 19.6.0 Time since boot: 6:21 Graphics/Displays: Intel Iris Pro: Chipset Model: Intel Iris Pro Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x0d26 Revision ID: 0x0008 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.0 chardet: 4.0.0 charset-normalizer: 2.0.4 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.28.1 ChimeraX-AtomicLibrary: 4.1.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.3 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.4 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202108221453 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.4 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.1 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0 ChimeraX-MDcrds: 2.5 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.1 ChimeraX-ModelPanel: 1.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.11.1 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.0.1 cycler: 0.10.0 Cython: 0.29.23 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.4.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.20 imagecodecs: 2021.4.28 imagesize: 1.2.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 2.11.3 jupyter-client: 6.1.12 jupyter-core: 4.7.1 kiwisolver: 1.3.1 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 1.1.1 matplotlib: 3.4.2 matplotlib-inline: 0.1.2 msgpack: 1.0.2 netCDF4: 1.5.6 networkx: 2.6.2 numexpr: 2.7.3 numpy: 1.21.0 numpydoc: 1.1.0 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.2.0 pip: 21.1.1 pkginfo: 1.7.0 prompt-toolkit: 3.0.20 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.9.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.2.1 qtconsole: 5.1.0 QtPy: 1.10.0 RandomWords: 0.3.0 requests: 2.25.1 scipy: 1.6.3 setuptools: 57.0.0 sfftk-rw: 0.7.0.post1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.0.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.26.6 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.2 wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
Component: | Unassigned → Sequence |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Bad sequence association |
comment:2 by , 4 years ago
Resolution: | → can't reproduce |
---|---|
Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Can't reproduce. The error is possibly the result of bad state due to previous errors. Hopefully fixing those will make this go away.