id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5907 Better starting directory when ChimeraX launched by file association Tristan Croll Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.3rc202112030319 (2021-12-03 03:19:12 UTC) Description Opened a ChimeraX session file by double-clicking in the Windows File Manager. Resultant working directory is c:\windows\system32. Doesn't seem ideal - wouldn't it be better to set it to the directory the session file is in? Log: UCSF ChimeraX version: 1.3rc202112030319 (2021-12-03) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:\\\Users\\\tristan\\\OneDrive - University of > Cambridge\\\Structures\\\Pu_Qian\\\r_palustris\\\PucA-LH2\\\working.cxs"" Opened zflip.mrc as #1.1.1.1, grid size 270,270,270, pixel 0.65, shown at level 0.014, step 1, values float32 Opened zflip.mrc gaussian as #1.1.1.2, grid size 270,270,270, pixel 0.66, shown at level 0.0108, step 1, values float32 Opened zflip.mrc zone as #5, grid size 270,270,270, pixel 0.66, shown at level 0.0233, step 1, values float32 Opened pucA_mask.mrc as #6, grid size 270,270,270, pixel 0.66, shown at level 0.000575, step 1, values float32 Log from Fri Dec 10 12:52:03 2021 > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.3rc202112030319 (2021-12-03) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > cd ""C:/Users/tristan/OneDrive - University of > Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2"" Current working directory is: C:\Users\tristan\OneDrive - University of Cambridge\Structures\Pu_Qian\r_palustris\PucA-LH2 > open ""C:/Users/tristan/OneDrive - University of > Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2/pucA-LH2GCMX- > ldao_real_space_refined_004.cif"" ""C:/Users/tristan/OneDrive - University of > Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2/zflip.mrc"" Summary of feedback from opening C:/Users/tristan/OneDrive - University of Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2/pucA-LH2GCMX- ldao_real_space_refined_004.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 735 Missing entity information. Treating each chain as a separate entity. Invalid residue range for struct_conf ""4"": invalid entity ""B"", near line 190 Invalid residue range for struct_conf ""5"": invalid entity ""B"", near line 191 Invalid residue range for struct_conf ""6"": invalid entity ""C"", near line 192 Invalid residue range for struct_conf ""7"": invalid entity ""C"", near line 193 Invalid residue range for struct_conf ""8"": invalid entity ""C"", near line 194 27 messages similar to the above omitted Atom H is not in the residue template for GLU /S:4 Atom C1 is not in the residue template for RDP /B:1797 Atom C1 is not in the residue template for RDP /D:1797 Atom C1 is not in the residue template for RDP /F:1797 Atom C1 is not in the residue template for RDP /H:1797 Atom C1 is not in the residue template for RDP /J:1797 4 messages similar to the above omitted Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' near line 13455 Skipping chem_comp category: Missing column 'type' near line 13613 Skipping chem_comp category: Missing column 'type' near line 14518 Skipping chem_comp category: Missing column 'type' near line 15207 notes | Fetching CCD LDA from http://ligand- expo.rcsb.org/reports/L/LDA/LDA.cif Fetching CCD RDP from http://ligand-expo.rcsb.org/reports/R/RDP/RDP.cif Chain information for pucA-LH2GCMX-ldao_real_space_refined_004.cif #1 --- Chain | Description A C E G I K M O Q | No description available B D F H J L N P R | No description available S | No description available Opened zflip.mrc as #2, grid size 270,270,270, pixel 0.66, shown at level 0.0156, step 2, values float32 > clipper associate #2 toModel #1 Opened zflip.mrc as #1.1.1.1, grid size 270,270,270, pixel 0.66, shown at level 0.0247, step 1, values float32 Chain information for pucA-LH2GCMX-ldao_real_space_refined_004.cif --- Chain | Description 1.2/A 1.2/C 1.2/E 1.2/G 1.2/I 1.2/K 1.2/M 1.2/O 1.2/Q | No description available 1.2/B 1.2/D 1.2/F 1.2/H 1.2/J 1.2/L 1.2/N 1.2/P 1.2/R | No description available 1.2/S | No description available > addh Summary of feedback from adding hydrogens to pucA-LH2GCMX- ldao_real_space_refined_004.cif #1.2 --- warning | Unknown hybridization for atom (C4) of residue type RDP; not adding hydrogens to it notes | No usable SEQRES records for pucA-LH2GCMX- ldao_real_space_refined_004.cif (#1.2) chain A; guessing termini instead No usable SEQRES records for pucA-LH2GCMX-ldao_real_space_refined_004.cif (#1.2) chain B; guessing termini instead No usable SEQRES records for pucA-LH2GCMX-ldao_real_space_refined_004.cif (#1.2) chain C; guessing termini instead No usable SEQRES records for pucA-LH2GCMX-ldao_real_space_refined_004.cif (#1.2) chain D; guessing termini instead No usable SEQRES records for pucA-LH2GCMX-ldao_real_space_refined_004.cif (#1.2) chain E; guessing termini instead 14 messages similar to the above omitted Chain-initial residues that are actual N termini: /A CXM 1, /B ALA 2, /C CXM 1, /D ALA 2, /E CXM 1, /F ALA 2, /G CXM 1, /H ALA 2, /I CXM 1, /J ALA 2, /K CXM 1, /L ALA 2, /M CXM 1, /N ALA 2, /O CXM 1, /P ALA 2, /Q CXM 1, /R ALA 2 Chain-initial residues that are not actual N termini: /S GLU 4 Chain-final residues that are actual C termini: /S ILE 97 Chain-final residues that are not actual C termini: /A ALA 50, /B HIS 47, /C ALA 50, /D HIS 47, /E ALA 50, /F HIS 47, /G ALA 50, /H HIS 47, /I ALA 50, /J HIS 47, /K ALA 50, /L HIS 47, /M ALA 50, /N HIS 47, /O ALA 50, /P HIS 47, /Q ALA 50, /R HIS 47 852 hydrogen bonds /A ALA 50 is not terminus, removing H atom from 'C' /B HIS 47 is not terminus, removing H atom from 'C' /C ALA 50 is not terminus, removing H atom from 'C' /D HIS 47 is not terminus, removing H atom from 'C' /E ALA 50 is not terminus, removing H atom from 'C' 13 messages similar to the above omitted 10089 hydrogens added > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 35 residues in model #1.2 to IUPAC-IUB standards. Done loading forcefield Loading residue template for LDA from internal database > ~hbonds Deleted the following atoms from residue BCL R1697: MG Deleted the following atoms from residue BCL R1598: MG Deleted the following atoms from residue BCL Q1702: MG Deleted the following atoms from residue BCL Q1502: MG Deleted the following atoms from residue BCL P1697: MG Deleted the following atoms from residue BCL P1598: MG Deleted the following atoms from residue BCL O1702: MG Deleted the following atoms from residue BCL O1502: MG Deleted the following atoms from residue BCL N1697: MG Deleted the following atoms from residue BCL N1598: MG Deleted the following atoms from residue BCL M1702: MG Deleted the following atoms from residue BCL M1502: MG Deleted the following atoms from residue BCL L1697: MG Deleted the following atoms from residue BCL L1598: MG Deleted the following atoms from residue BCL K1702: MG Deleted the following atoms from residue BCL K1502: MG Deleted the following atoms from residue BCL J1697: MG Deleted the following atoms from residue BCL J1598: MG Deleted the following atoms from residue BCL I1702: MG Deleted the following atoms from residue BCL I1502: MG Deleted the following atoms from residue BCL H1697: MG Deleted the following atoms from residue BCL H1598: MG Deleted the following atoms from residue BCL G1702: MG Deleted the following atoms from residue BCL G1502: MG Deleted the following atoms from residue BCL F1598: MG, HGA Deleted the following atoms from residue BCL E1702: MG Deleted the following atoms from residue BCL E1502: MG Deleted the following atoms from residue BCL D1598: MG Deleted the following atoms from residue BCL C1702: MG Deleted the following atoms from residue BCL C1502: MG Deleted the following atoms from residue BCL B1598: MG Deleted the following atoms from residue BCL A1702: MG Deleted the following atoms from residue BCL A1502: MG > isolde parameterise sel Running ANTECHAMBER command: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\tristan\AppData\Local\Temp\tmpm6go_7am\ante.in.mol2 -fi mol2 -o C:\Users\tristan\AppData\Local\Temp\tmpm6go_7am\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (RDP) `` (RDP) `Welcome to antechamber 20.0: molecular input file processor.` (RDP) `` (RDP) `Info: Finished reading file (C:\Users\tristan\AppData\Local\Temp\tmpm6go_7am\ante.in.mol2); atoms read (99), bonds read (98).` (RDP) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (RDP) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (RDP) `bash.exe: warning: could not find /tmp, please create!` (RDP) `` (RDP) `` (RDP) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (RDP) `bash.exe: warning: could not find /tmp, please create!` (RDP) `Info: Total number of electrons: 306; net charge: 0` (RDP) `` (RDP) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out` (RDP) `bash.exe: warning: could not find /tmp, please create!` (RDP) `` (RDP) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc"" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p ""C:/Program Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT"" -s 2 -j 1` (RDP) `bash.exe: warning: could not find /tmp, please create!` (RDP) `` (RDP) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (RDP) `bash.exe: warning: could not find /tmp, please create!` (RDP) `` Charges for residue RDP determined OpenMM ffXML file RDP written to the current working directory. New template added to forcefield as USER_RDP. This ligand should now work in all remaining simulations for this session. To use in future sessions, load the ffXML file with ISOLDE's Load Residue MD Definition(s) button. > delete sel [Repeated 1 time(s)] > set bgColor white > hide HC > dssp > select #1 22381 atoms, 22821 bonds, 2 pseudobonds, 1034 residues, 13 models selected > select #1 22381 atoms, 22821 bonds, 2 pseudobonds, 1034 residues, 16 models selected ISOLDE: started sim > select clear ISOLDE: paused sim ISOLDE: resumed sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 10 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select up 47 atoms, 46 bonds, 1 residue, 1 model selected > delete sel > st first > volume gaussian #1 bfactor 50 Opened zflip.mrc gaussian as #2, grid size 270,270,270, pixel 0.66, shown at step 1, values float32 > clipper associate #2 toModel #1 Opened zflip.mrc gaussian as #1.1.1.2, grid size 270,270,270, pixel 0.66, shown at step 1, values float32 > cs 0.25 > select up 140 atoms, 148 bonds, 1 residue, 1 model selected > delete sel > ui tool show ""Show Sequence Viewer"" > st /A Multiple residues selected! Going to the first... > select /A 1087 atoms, 1115 bonds, 52 residues, 1 model selected ISOLDE: started sim ISOLDE: paused sim > st [Repeated 3 time(s)]ISOLDE: resumed sim ISOLDE: paused sim > st [Repeated 2 time(s)]ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /B 965 atoms, 982 bonds, 48 residues, 1 model selected ISOLDE: started sim ISOLDE: paused sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /A,B 2052 atoms, 2097 bonds, 100 residues, 1 model selected ISOLDE: started sim ISOLDE: paused sim > select clear > st [Repeated 7 time(s)]ISOLDE: resumed sim ISOLDE: paused sim > st [Repeated 1 time(s)]ISOLDE: resumed sim ISOLDE: paused sim > st [Repeated 5 time(s)]ISOLDE: resumed sim ISOLDE: paused sim > st [Repeated 3 time(s)]ISOLDE: resumed sim ISOLDE: paused sim ISOLDE: resumed sim ISOLDE: paused sim > st [Repeated 7 time(s)]ISOLDE: resumed sim ISOLDE: paused sim > st [Repeated 5 time(s)]ISOLDE: resumed sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > awsf > select /A,B 2055 atoms, 2099 bonds, 101 residues, 1 model selected ISOLDE: started sim ISOLDE: paused sim > st [Repeated 4 time(s)]ISOLDE: resumed sim > st [Repeated 47 time(s)]ISOLDE: paused sim ISOLDE: resumed sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim Added a C-terminal OXT to chain B ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save pucA_working.cxs Taking snapshot of stepper: pucA-LH2GCMX-ldao_real_space_refined_004.cif > ui tool show Shell > select protein&~/S 13798 atoms, 13996 bonds, 864 residues, 1 model selected > usage sym sym structures [symmetry] [center center point] [axis an axis vector] [coordinateSystem a coordinate-system] [contact a number] [range a number] [assembly a text string] [copies true or false] [newModel true or false] [surfaceOnly true or false] [resolution a number] [gridSpacing a number] — create model copies symmetry: symmetry sym clear [structures] — Remove model copies > select clear > select /A,B 2056 atoms, 2100 bonds, 101 residues, 1 model selected > select :BCL 4480 atoms, 4737 bonds, 32 residues, 1 model selected > select clear > select /A,B 2056 atoms, 2100 bonds, 101 residues, 1 model selected > select clear > select /A,B 2056 atoms, 2100 bonds, 101 residues, 1 model selected Chain information for ASU #2 --- Chain | Description A | No description available B | No description available > ui tool show ""Show Sequence Viewer"" > sym #2 C9 axis 0,0,1 center 89.34,88.99,86.23 > close #3 > ui tool show ""Show Sequence Viewer"" > sym #2 C8 axis 0,0,1 center 89.34,88.99,86.23 > close #3 > sym #2 C9 axis 0,0,1 center 89.34,88.99,86.23 > select #1/A,B 2056 atoms, 2100 bonds, 101 residues, 1 model selected > hide #!3 models > show #2 models > delete #1&~/A,B,S > hide #2 models > show #!3 models > hide #3.1 models > close #3.1 > select #3 16448 atoms, 16800 bonds, 808 residues, 9 models selected ISOLDE: merge models Merging models #3.2,#3.3,#3.4,#3.5,#3.6,#3.7,#3.8,#3.9 into #1.2. Remapping chain ID A in #3.2 to C Remapping chain ID B in #3.2 to D Remapping chain ID A in #3.3 to E Remapping chain ID B in #3.3 to F Remapping chain ID A in #3.4 to G Remapping chain ID B in #3.4 to H Remapping chain ID A in #3.5 to I Remapping chain ID B in #3.5 to J Remapping chain ID A in #3.6 to K Remapping chain ID B in #3.6 to L Remapping chain ID A in #3.7 to M Remapping chain ID B in #3.7 to N Remapping chain ID A in #3.8 to O Remapping chain ID B in #3.8 to P Remapping chain ID A in #3.9 to Q Remapping chain ID B in #3.9 to R > hide #!3 models > isolde restrain torsions #1&~/S The ""isolde restrain torsions"" command only applies to protein chains. Other residues have been ignored. ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > select #1 19979 atoms, 20394 bonds, 1003 residues, 21 models selected > isolde restrain distances #1 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: started sim > select clear ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select #1 19979 atoms, 20394 bonds, 1003 residues, 21 models selected > rd > select clear > st /A Multiple residues selected! Going to the first... > st [Repeated 45 time(s)]ISOLDE: started sim > select clear ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 48 time(s)] > select :RDP 1782 atoms, 1764 bonds, 18 residues, 10 models selected > select /A,B:RDP 990 atoms, 980 bonds, 10 residues, 10 models selected > select #1/A,B:RDP 99 atoms, 98 bonds, 1 residue, 1 model selected > close #3 > ui mousemode right ""translate selected atoms"" > isolde ignore #1&~sel ISOLDE: currently ignoring 1002 residues in model 1.2 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde ~ignore ISOLDE: started sim > select clear [Repeated 1 time(s)]ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select up 99 atoms, 98 bonds, 1 residue, 1 model selected > close #2 > sym #3 C9 axis 0,0,1 center 89.34,88.99,86.23 > view /D:RDP > select clear > close #2 > close #3 > select up 99 atoms, 98 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected atoms"" > isolde ignore ~sel ISOLDE: currently ignoring 1002 residues in model 1.2 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde ~ignore > select /F:RDP 99 atoms, 98 bonds, 1 residue, 1 model selected > view sel > ui mousemode right ""translate selected atoms"" > isolde ignore ~sel ISOLDE: currently ignoring 1002 residues in model 1.2 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde ~ignore > select /H:RDP 99 atoms, 98 bonds, 1 residue, 1 model selected > view sel > ui mousemode right ""translate selected atoms"" > isolde ignore ~sel ISOLDE: currently ignoring 1002 residues in model 1.2 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde ~ignore > select /J:RDP 99 atoms, 98 bonds, 1 residue, 1 model selected > view sel > ui mousemode right ""translate selected atoms"" > isolde ignore ~sel ISOLDE: currently ignoring 1002 residues in model 1.2 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde ~ignore > select /L:RDP 99 atoms, 98 bonds, 1 residue, 1 model selected > view sel > ui mousemode right ""translate selected atoms"" > isolde ignore ~sel ISOLDE: currently ignoring 1002 residues in model 1.2 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde ~ignore ISOLDE: started sim > select clear ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /N:RDP 99 atoms, 98 bonds, 1 residue, 1 model selected > view sel > ui mousemode right ""translate selected atoms"" > isolde ignore ~sel ISOLDE: currently ignoring 1002 residues in model 1.2 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde ~ignore ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /P:RDP 99 atoms, 98 bonds, 1 residue, 1 model selected > view sel > ui mousemode right ""translate selected atoms"" > isolde ignore ~sel ISOLDE: currently ignoring 1002 residues in model 1.2 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde ~ignore ISOLDE: started sim > select clear ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /R:RDP 99 atoms, 98 bonds, 1 residue, 1 model selected > view sel > ui mousemode right ""translate selected atoms"" > select up 966 atoms, 983 bonds, 48 residues, 1 model selected > select down 99 atoms, 98 bonds, 1 residue, 1 model selected > isolde ignore ~sel ISOLDE: currently ignoring 1002 residues in model 1.2 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde ~ignore ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save working.cxs Taking snapshot of stepper: pucA-LH2GCMX-ldao_real_space_refined_004.cif > select #1 19979 atoms, 20394 bonds, 1003 residues, 21 models selected > select clear > open C:/Users/tristan/Downloads/working.pdb Chain information for working.pdb #2 --- Chain | Description A | No description available B E I K N Q T W Z | No description available D G H M P S V Y | No description available O | No description available > matchmaker #2/A to #1/A Parameters --- Chain pairing | bb 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 pucA-LH2GCMX-ldao_real_space_refined_004.cif, chain A (#1.2) with working.pdb, chain A (#2), sequence alignment score = 221.9 RMSD between 48 pruned atom pairs is 0.410 angstroms; (across all 50 pairs: 2.142) > cartoon #2 > hide #2 > matchmaker #2/O to #1/S Parameters --- Chain pairing | bb 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 pucA-LH2GCMX-ldao_real_space_refined_004.cif, chain S (#1.2) with working.pdb, chain O (#2), sequence alignment score = 426 RMSD between 75 pruned atom pairs is 1.016 angstroms; (across all 91 pairs: 1.734) > show #2/O > style stick Changed 41279 atom styles > isolde restrain torsions #1/S templateResidues #2/O ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... [Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 8 residues in model #2 to IUPAC-IUB standards. > hide #!2 models > select #1/S 1475 atoms, 1494 bonds, 94 residues, 1 model selected ISOLDE: started sim ISOLDE: paused sim ISOLDE: resumed sim > show #!2 models > hide #!2 models ISOLDE: paused sim ISOLDE: resumed sim > rt ISOLDE: paused sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select #1/S 1475 atoms, 1494 bonds, 94 residues, 1 model selected > save s.pdb #1 selectedOnly true > open s.pdb Summary of feedback from opening s.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 4 THR A 8 1 5 Start residue of secondary structure not found: HELIX 2 2 PRO A 12 HIS A 37 1 26 Start residue of secondary structure not found: HELIX 3 3 TRP A 40 ASN A 46 1 7 Start residue of secondary structure not found: HELIX 4 4 VAL B 11 TYR B 42 1 32 Start residue of secondary structure not found: HELIX 5 5 ALA C 4 THR C 8 1 5 31 messages similar to the above omitted Chain information for s.pdb #3 --- Chain | Description S | No description available > sym #3 C9 axis 0,0,1 center 89.34,88.99,86.23 > select #1 19979 atoms, 20394 bonds, 1003 residues, 21 models selected > show #4 > hide HC > usage color bymodel color [objects] [color [what]] [target characters from 'abcfmprs'] [transparency a number] [halfbond true or false] — color objects objects: an objects specifier or nothing color: a color or one of byatom, bychain, byelement, byhetero, byidentity, bymodel, bynucleotide, bypolymer, fromatoms, or random what: a collection of one of All, atoms, bonds, cartoons, labels, models, pseudobonds, ribbons, rings, or surfaces Subcommands are: * color bfactor * color byattribute * color cylindrical * color delete * color electrostatic * color gradient * color height * color image * color list * color modify * color name * color radial * color sample * color sequential * color show * color single * color zone > select #4 13275 atoms, 13446 bonds, 846 residues, 10 models selected > ~cartoon #4 > cartoon #4 > select clear > hide #4 models > show #4.8 models > select clear > show #4.1 models > show #4.2 models > show #4.3 models > show #4.4 models > show #4.5 models > show #4.6 models > show #4.7 models > show #4.9 models > usage vol mask volume mask volumes surfaces a surfaces specifier [pad a number] [extend an integer] [fullMap true or false] [slab slab] [invertMask true or false] [axis an axis vector] [sandwich true or false] [fillOverlap true or false] [modelId modelId] — Mask a map to a surface slab: a number or some numbers modelId: a model id > usage vol onesmask volume onesmask surfaces [onGrid a density map specifier] [spacing 1 or 3 floats] [border a number] [valueType numeric value type] [pad a number] [extend an integer] [fullMap true or false] [slab slab] [invertMask true or false] [axis an axis vector] [sandwich true or false] [fillOverlap true or false] [modelId modelId] — Make a mask of 1 values for a surface slab: a number or some numbers modelId: a model id > usage vol volume [volumes] [style style] [change change] [show] [hide] [toggle] [close close] [level level] [rmsLevel rmsLevel] [sdLevel sdLevel] [encloseVolume encloseVolume] [fastEncloseVolume fastEncloseVolume] [color color] [brightness a number] [transparency a number] [appearance appearance] [nameAppearance a text string] [nameForget nameForget] [step map step] [region map region] [expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex 1 or 3 floats] [voxelSize 1 or 3 floats] [planes planes x|y|z[,[,[,[,]]]]] [dumpHeader true or false] [pickable true or false] [symmetry symmetry] [center center point] [centerIndex 1 or 3 floats] [axis an axis vector] [coordinateSystem a coordinate-system] [dataCacheSize a number] [showOnOpen true or false] [voxelLimitForOpen a number] [showPlane true or false] [voxelLimitForPlane a number] [showOutlineBox true or false] [outlineBoxRgb a color] [limitVoxelCount true or false] [voxelLimit a number] [colorMode colorMode] [colormapOnGpu true or false] [colormapSize an integer] [colormapExtendLeft true or false] [colormapExtendRight true or false] [backingColor backingColor] [blendOnGpu true or false] [projectionMode projectionMode] [planeSpacing planeSpacing] [fullRegionOnGpu true or false] [btCorrection true or false] [minimalTextureMemory true or false] [maximumIntensityProjection true or false] [linearInterpolation true or false] [dimTransparency true or false] [dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting true or false] [twoSidedLighting true or false] [flipNormals true or false] [subdivideSurface true or false] [subdivisionLevels an integer] [surfaceSmoothing true or false] [smoothingIterations an integer] [smoothingFactor a number] [squareMesh true or false] [capFaces true or false] [boxFaces true or false] [orthoplanes orthoplanes] [positionPlanes positionPlanes] [tiltedSlab true or false] [tiltedSlabAxis an axis vector] [tiltedSlabOffset a number] [tiltedSlabSpacing a number] [tiltedSlabPlaneCount an integer] [imageMode imageMode] [calculateSurfaces true or false] — set volume model parameters, display style and colors style: one of image, mesh, solid, or surface change: one of image or surface close: one of image or surface level: some numbers, repeatable rmsLevel: some numbers, repeatable sdLevel: some numbers, repeatable encloseVolume: some numbers fastEncloseVolume: some numbers color: a color, repeatable appearance: one of Airways, airways, Airways II, Black & White, Bone + Skin, Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs, CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone, Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II, Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow Bone nameForget: one of Airways, airways, Airways II, Black & White, Bone + Skin, Bone + Skin II, brain, chest, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs, CT_Muscles, CT_Skin, CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone, Glossy, Glossy II, Gold Bone, High Contrast, initial, Low Contrast, Mid Contrast, No Shading, Pencil, Red on White, Skin On Blue, Skin On Blue II, Soft, Soft + Skin, Soft + Skin II, Soft + Skin III, Soft On Blue, Soft on White, Standard, Vascular, Vascular II, Vascular III, Vascular IV, or Yellow Bone colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16, la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8, rgba12, rgba16, rgba4, or rgba8 backingColor: a color or none projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, or auto planeSpacing: one of max, mean, or min or a number orthoplanes: one of off, xy, xyz, xz, or yz positionPlanes: some integers imageMode: one of box faces, full region, orthoplanes, or tilted slab Subcommands are: * volume add * volume bin * volume boxes * volume channels * volume copy * volume cover * volume erase * volume falloff * volume flatten * volume flip * volume fourier * volume gaussian * volume laplacian * volume localCorrelation * volume mask * volume maximum * volume median * volume minimum * volume morph * volume multiply * volume new * volume octant * volume ~octant * volume onesmask * volume permuteAxes * volume resample * volume ridges * volume scale * volume settings * volume splitbyzone * volume subtract * volume threshold * volume tile * volume unbend * volume unroll * volume unzone * volume zone > usage vol zone volume zone volumes nearAtoms an atoms specifier [range a number] [bondPointSpacing a number] [minimalBounds true or false] [newMap true or false] [invert true or false] [subregion map region] [step map step] [modelId modelId] — Zero map values beyond a distance range from atoms modelId: a model id > volume zone #1.1.1.1 nearAtoms #4 range 12 newMap true Opened zflip.mrc zone as #5, grid size 270,270,270, pixel 0.66, shown at step 1, values float32 > close #5 > volume zone #1.1.1.1 nearAtoms #4 range 6 newMap true Opened zflip.mrc zone as #5, grid size 270,270,270, pixel 0.66, shown at step 1, values float32 > volume gaussian #5 bfactor 200 Opened zflip.mrc zone gaussian as #6, grid size 270,270,270, pixel 0.66, shown at step 1, values float32 > volume #6 level 0.000657 > volume #6 level 0.002705 > volume #6 level 0.003279 > volume #6 level 0.0005751 > select clear > clipper spotlight radius 13.00 > clipper spotlight radius 14.00 > clipper spotlight radius 15.00 > clipper spotlight radius 16.00 > clipper spotlight radius 17.00 > clipper spotlight radius 18.00 ISOLDE: started sim > hide #!4 models ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 12 time(s)]ISOLDE: started sim > select clear ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1 19979 atoms, 20394 bonds, 1003 residues, 21 models selected ISOLDE: started sim > select clear [Repeated 1 time(s)]ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 23 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view /A:37 > view #1/A:37 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 1 time(s)]ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 8 time(s)]ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 14 time(s)]ISOLDE: started sim > rt > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > aw > isolde sim start sel ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > delete sel ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 5 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view > view #1/B:20 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 37 time(s)]ISOLDE: started sim > select clear ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 8 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 16 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 1 time(s)]ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 33 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 41 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 17 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 15 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 7 time(s)] > rt > st [Repeated 5 time(s)] > select clear > st [Repeated 4 time(s)] > rt ISOLDE: started sim > select clear ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > rt > st [Repeated 36 time(s)]ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 2 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 1 time(s)]ISOLDE: started sim > select clear ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 18 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 59 time(s)]ISOLDE: started sim Traceback (most recent call last): File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2096, in _next_rotamer target_def = rrm.next_preview(rot) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\molobject.py"", line 4438, in next_preview return self._incr_preview(rotamer, 1) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\molobject.py"", line 4420, in _incr_preview new_target = (current_target + incr) % num_targets ZeroDivisionError: integer division or modulo by zero ZeroDivisionError: integer division or modulo by zero File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\molobject.py"", line 4420, in _incr_preview new_target = (current_target + incr) % num_targets See log for complete Python traceback. > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 18 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 16 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 60 time(s)]ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 8 time(s)]ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 8 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view #1/A:20 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view #1/C:20 > view #1/E:20 > st [Repeated 16 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 20 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 4 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 10 time(s)]ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 23 time(s)]ISOLDE: started sim > select clear > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 11 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 22 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 4 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 18 time(s)]ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 3 time(s)]ISOLDE: started sim > select clear > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 32 time(s)]ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 34 time(s)]ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > ht ND Set protonation of HIS #1.2/Q:37 to ND ISOLDE: started sim > select clear [Repeated 1 time(s)]ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > st [Repeated 26 time(s)]ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > rt > st [Repeated 32 time(s)] > select #1&~protein&~:HOH 4671 atoms, 4878 bonds, 36 residues, 21 models selected > clipper spotlight radius 17.00 > clipper spotlight radius 16.00 ISOLDE: started sim > select clear ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > show #!6 models > save pucA_mask.mrc #6 > volume #6 style image region 0,0,0,269,269,269 step 2 colorMode opaque8 > showOutlineBox true imageMode ""box faces"" > volume #6 style surface region 0,0,0,269,269,269 step 1 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1 19979 atoms, 20394 bonds, 1003 residues, 21 models selected > open ""C:/Users/tristan/OneDrive - University of > Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2/pucA-LH2GCMX- > ldao_real_space_refined_004.cif"" Summary of feedback from opening C:/Users/tristan/OneDrive - University of Cambridge/Structures/Pu_Qian/r_palustris/PucA-LH2/pucA-LH2GCMX- ldao_real_space_refined_004.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 735 Missing entity information. Treating each chain as a separate entity. Invalid residue range for struct_conf ""4"": invalid entity ""B"", near line 190 Invalid residue range for struct_conf ""5"": invalid entity ""B"", near line 191 Invalid residue range for struct_conf ""6"": invalid entity ""C"", near line 192 Invalid residue range for struct_conf ""7"": invalid entity ""C"", near line 193 Invalid residue range for struct_conf ""8"": invalid entity ""C"", near line 194 27 messages similar to the above omitted Atom H is not in the residue template for GLU /S:4 Atom C1 is not in the residue template for RDP /B:1797 Atom C1 is not in the residue template for RDP /D:1797 Atom C1 is not in the residue template for RDP /F:1797 Atom C1 is not in the residue template for RDP /H:1797 Atom C1 is not in the residue template for RDP /J:1797 4 messages similar to the above omitted Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' near line 13455 Skipping chem_comp category: Missing column 'type' near line 13613 Skipping chem_comp category: Missing column 'type' near line 14518 Skipping chem_comp category: Missing column 'type' near line 15207 Chain information for pucA-LH2GCMX-ldao_real_space_refined_004.cif #7 --- Chain | Description A C E G I K M O Q | No description available B D F H J L N P R | No description available S | No description available > hide #7&~:BCL > select clear [Repeated 1 time(s)] > hide #!1 models > select #7/H 670 atoms, 687 bonds, 36 pseudobonds, 49 residues, 3 models selected > select #7/H:1697 140 atoms, 144 bonds, 4 pseudobonds, 1 residue, 2 models selected > select #7:1697 840 atoms, 864 bonds, 24 pseudobonds, 6 residues, 2 models selected > delete #7&~sel > show #!1 models > save working.cxs\ 'working.cxs\' has only compression suffix; cannot determine format from suffix > save working.cxs Taking snapshot of stepper: pucA-LH2GCMX-ldao_real_space_refined_004.cif ISOLDE: merge models Merging models #7 into #1.2. Remapping chain ID H in #7 to T Remapping chain ID J in #7 to U Remapping chain ID L in #7 to V Remapping chain ID N in #7 to W Remapping chain ID P in #7 to X Remapping chain ID R in #7 to Y > hide #!7 models ISOLDE: stopped sim Deleted the following atoms from residue BCL Y1697: MG Deleted the following atoms from residue BCL X1697: MG Deleted the following atoms from residue BCL W1697: MG Deleted the following atoms from residue BCL V1697: MG Deleted the following atoms from residue BCL U1697: MG Deleted the following atoms from residue BCL T1697: MG ISOLDE: started sim ISOLDE: paused sim > ui mousemode right ""translate selected atoms"" > select up 140 atoms, 148 bonds, 1 residue, 1 model selected ISOLDE: resumed sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > aw > isolde sim start sel ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > delete sel > volume gaussian #1.1.1.1 bfactor 150 Opened zflip.mrc gaussian as #8, grid size 270,270,270, pixel 0.66, shown at step 1, values float32 > close #8 > show #!1.1.1.1 models ISOLDE: started sim > select clear ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim > rt ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save working.cxs Taking snapshot of stepper: pucA-LH2GCMX-ldao_real_space_refined_004.cif ——— End of log from Fri Dec 10 12:52:03 2021 ——— opened ChimeraX session > pwd Current working directory is: C:\windows\system32 OpenGL version: 3.3.0 NVIDIA 497.29 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Notebook Model: P7xxTM1 OS: Microsoft Windows 10 Education (Build 19041) Memory: 68,654,501,888 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz OSLanguage: en-GB Locale: ('en_GB', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: -: imerax-clipper -himerax-clipper: 0.17.0 -himerax-isolde: 1.3.dev33 alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.8 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 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: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3rc202112030319 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 2.1.2 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-ISOLDE: 1.3 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: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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: 2.4.6 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: 1.6.1 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: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 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: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 python-igraph: 0.9.7 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 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 tables: 3.6.1 texttable: 1.6.4 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 versioneer: 0.21 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " enhancement reopened normal Input/Output Greg Couch Eric Pettersen all ChimeraX