id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10362 Mouse modes goes bananas Tristan Croll Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.7rc202311140124 (2023-11-14 01:24:52 UTC) Description Merged a ligand generated from SMILES (which is loaded with a chain ID of ""?"") into ISOLDE's working model. Used the ""bond rotation"" mouse mode on it, leading to the error ""Must specify exactly 4 atoms for 'torsion' command; you specified 8"" being spammed to the log (it does actually still rotate the bond, though). That's not the fun part, though: it's left the session completely borked, with *every* mouse button (with or without modifier keys) all going to rotation of the bond I originally clicked, even though that mouse mode is no longer assigned to anything (see below - note that the modes with the generic ""mode name"" are Clipper modes... I'll see about fixing that): for b in session.ui.mouse_modes.bindings: print(f'{b.modifiers}-{b.button}: {b.mode.name}') []-middle: translate []-pause: identify object ['control']-left: select ['control', 'shift']-left: select add ['control', 'alt']-left: select subtract ['shift']-right: zoom []-wheel: zoom ['shift']-wheel: mode name ['control']-middle: mode name ['control']-wheel: mode name ['alt']-wheel: mode name []-left: rotate []-right: isolde tug atom Log: > 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: 1.7rc202311140124 (2023-11-14) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7pe8 Summary of feedback from opening 7pe8 fetched from pdb --- note | Fetching compressed mmCIF 7pe8 from http://files.rcsb.org/download/7pe8.cif 7pe8 title: cryo-EM structure of DEPTOR bound to human mTOR complex 2, focussed on one protomer [more info...] Chain information for 7pe8 #1 --- Chain | Description | UniProt A | Serine/threonine-protein kinase mTOR | MTOR_HUMAN 1-2549 C | Target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326 E | Rapamycin-insensitive companion of mTOR | RICTR_HUMAN 1-1708 G | Target of rapamycin complex 2 subunit MAPKAP1 | SIN1_HUMAN 1-522 I | DEP domain-containing mTOR-interacting protein | DPTOR_HUMAN 1-409 Non-standard residues in 7pe8 #1 --- ACE — acetyl group IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) ZN — zinc ion > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 203 residues in model #1 to IUPAC-IUB standards. 7pe8 title: cryo-EM structure of DEPTOR bound to human mTOR complex 2, focussed on one protomer [more info...] Chain information for 7pe8 --- Chain | Description | UniProt 1.2/A | Serine/threonine-protein kinase mTOR | MTOR_HUMAN 1-2549 1.2/C | Target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326 1.2/E | Rapamycin-insensitive companion of mTOR | RICTR_HUMAN 1-1708 1.2/G | Target of rapamycin complex 2 subunit MAPKAP1 | SIN1_HUMAN 1-522 1.2/I | DEP domain-containing mTOR-interacting protein | DPTOR_HUMAN 1-409 Non-standard residues in 7pe8 #1.2 --- ACE — acetyl group IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) ZN — zinc ion > log metadata #1.2 Metadata for 7pe8 #1.2 --- Title | cryo-EM structure of DEPTOR bound to human mTOR complex 2, focussed on one protomer Citations | Walchli, M., Berneiser, K., Mangia, F., Imseng, S., Craigie, L.M., Stuttfeld, E., Hall, M.N., Maier, T. (2021). Regulation of human mTOR complexes by DEPTOR. Elife, 10. PMID: 34519268. DOI: 10.7554/eLife.70871 (2018). ISOLDE: a physically realistic environment for model building into low-resolution electron density maps. Acta Cryst. D, 74(6), 519-530. PMID: 29872003. DOI: 10.1107/S2059798318002425 Non-standard residues | ACE — acetyl group IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) ZN — zinc ion Gene source | Homo sapiens (human) CryoEM Map | EMDB 13348 — open map Experimental method | Electron microscopy Resolution | 3.20Å > open 13348 fromDatabase emdb Summary of feedback from opening 13348 fetched from emdb --- notes | Fetching compressed map 13348 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-13348/map/emd_13348.map.gz Fetching map header 13348 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-13348/header/emd-13348.xml open kw {'initial_surface_level': 0.185} Opened emdb 13348 as #2, grid size 480,480,480, pixel 1.06, shown at level 0.185, step 2, values float32, fit PDB 7pe8 > clipper associate #2 toModel #1 Opened emdb 13348 as #1.1.1.1, grid size 480,480,480, pixel 1.06, shown at step 1, values float32 > select :IHP 36 atoms, 36 bonds, 1 residue, 1 model selected > view sel > rainbow /C > open 4jsn Summary of feedback from opening 4jsn fetched from pdb --- note | Fetching compressed mmCIF 4jsn from http://files.rcsb.org/download/4jsn.cif 4jsn title: structure of mTORdeltaN-mLST8 complex [more info...] Chain information for 4jsn #2 --- Chain | Description | UniProt A B | Serine/threonine-protein kinase mTOR | MTOR_HUMAN 1376-2549 C D | Target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326 4jsn mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > matchmaker #2 to #1/C 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 7pe8, chain C (#1.2) with 4jsn, chain D (#2), sequence alignment score = 1636.7 RMSD between 293 pruned atom pairs is 0.880 angstroms; (across all 317 pairs: 1.609) > close > alphafold fetch Q8N2K0 Chain information for AlphaFold Q8N2K0 #1 --- Chain | Description | UniProt A | Lysophosphatidylserine lipase ABHD12 | ABD12_HUMAN 1-398 Color AlphaFold Q8N2K0 by residue attribute pLDDT_score > show > color byhetero > select :75-95 161 atoms, 165 bonds, 21 residues, 1 model selected > style sel sphere Changed 161 atom styles > style sel ball Changed 161 atom styles > ui tool show ""2D Builder"" Please register the custom scheme 'editor' via QWebEngineUrlScheme::registerScheme() before installing the custom scheme handler. > isolde select #1 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 67 residues in model #1 to IUPAC-IUB standards. Chain information for AlphaFold Q8N2K0 --- Chain | Description | UniProt 1.2/A | Lysophosphatidylserine lipase ABHD12 | ABD12_HUMAN 1-398 Color AlphaFold Q8N2K0 by residue attribute pLDDT_score ISOLDE: attempting to load PAE matrix for model #1.2 from the AlphaFold-EBI database. If this fails or you wish to use a different PAE matrix, use the ""Load PAE matrix"" button in ISOLDE's reference model restraints widget. > alphafold pae #1.2 uniprotId Q8N2K0 plot false Fetching compressed AlphaFold PAE Q8N2K0 from https://alphafold.ebi.ac.uk/files/AF-Q8N2K0-F1-predicted_aligned_error_v4.json s1: MRKRTEPVALEHERCAAAGSSSSGSAAAALDADCRLKQNLRLTGPAAAEPRCAADAGMKRALGRRKGVWLRLRKILFCVLGLYIAIPFLIKLCPGIQAKLIFLNFVRVPYFIDLKKPQDQGLNHTCNYYLQPEEDVTIGVWHTVPAVWWKNAQGKDQMWYEDALASSHPIILYLHGNAGTRGGDHRVELYKVLSSLGYHVVTFDYRGWGDSVGTPSERGMTYDALHVFDWIKARSGDNPVYIWGHSLGTGVATNLVRRLCERETPPDALILESPFTNIREEAKSHPFSVIYRYFPGFDWFFLDPITSSGIKFANDENVKHISCPLLILHAEDDPVVPFQLGRKLYSIAAPARSFRDFKVQFVPFHSDLGYRHKYIYKSPELPRILREFLGKSEPEHQH s2: MRKRTEPVALEHERCAAAGSSSSGSAAAALDADCRLKQNLRLTGPAAAEPRCAADAGMKRALGRRKGVWLRLRKILFCVLGLYIAIPFLIKLCPGIQAKLIFLNFVRVPYFIDLKKPQDQGLNHTCNYYLQPEEDVTIGVWHTVPAVWWKNAQGKDQMWYEDALASSHPIILYLHGNAGTRGGDHRVELYKVLSSLGYHVVTFDYRGWGDSVGTPSERGMTYDALHVFDWIKARSGDNPVYIWGHSLGTGVATNLVRRLCERETPPDALILESPFTNIREEAKSHPFSVIYRYFPGFDWFFLDPITSSGIKFANDENVKHISCPLLILHAEDDPVVPFQLGRKLYSIAAPARSFRDFKVQFVPFHSDLGYRHKYIYKSPELPRILREFLGKSEPEHQH > isolde restrain distances ""#1.2/A"" templateAtoms ""#1.2/A"" perChain false > adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff > 2.50 groupName ""Reference Distance Restraints"" ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > isolde restrain torsions #1.2/A templateResidues #1.2/A adjustForConfidence > true sidechains true springConstant 250.00 alpha 0.20 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > select :75-95 161 atoms, 165 bonds, 21 residues, 1 model selected > style sel ball Changed 161 atom styles > clipper isolate #1 > select #2 56 atoms, 59 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected atoms"" ISOLDE: merge models Merging models #2 into #1.2. > hide #2 models > select up 56 atoms, 59 bonds, 1 residue, 1 model selected > isolde parameterise sel UNK: number of electrons (286) + formal charge (+1) is odd; cannot compute charges for radical species using AM1-BCC method > show sel > select up 57 atoms, 60 bonds, 1 residue, 1 model selected > isolde parameterise sel netCharge 1 Running ANTECHAMBER command: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\TRISTA~1\AppData\Local\Temp\tmpg9pexs8x\ante.in.mol2 -fi mol2 -o C:\Users\TRISTA~1\AppData\Local\Temp\tmpg9pexs8x\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (UNK) `` (UNK) `Welcome to antechamber 20.0: molecular input file processor.` (UNK) `` (UNK) `Info: Finished reading file (C:\Users\TRISTA~1\AppData\Local\Temp\tmpg9pexs8x\ante.in.mol2); atoms read (57), bonds read (60).` (UNK) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (UNK) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (UNK) `bash.exe: warning: could not find /tmp, please create!` (UNK) `` (UNK) `` (UNK) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (UNK) `bash.exe: warning: could not find /tmp, please create!` (UNK) `Info: Total number of electrons: 286; net charge: 1` (UNK) `` (UNK) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out` (UNK) `bash.exe: warning: could not find /tmp, please create!` (UNK) `` (UNK) `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` (UNK) `bash.exe: warning: could not find /tmp, please create!` (UNK) `` (UNK) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (UNK) `bash.exe: warning: could not find /tmp, please create!` (UNK) `` Charges for residue UNK determined OpenMM ffXML file UNK written to the current working directory. New template added to forcefield as USER_UNK. 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. > addh protein Summary of feedback from adding hydrogens to AlphaFold Q8N2K0 #1.2 --- notes | Termini for AlphaFold Q8N2K0 (#1.2) chain A determined from SEQRES records Chain-initial residues that are actual N termini: AlphaFold Q8N2K0 #1.2/A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: AlphaFold Q8N2K0 #1.2/A HIS 398 Chain-final residues that are not actual C termini: 353 hydrogen bonds 3154 hydrogens added > select up 57 atoms, 60 bonds, 1 residue, 1 model selected > select zone sel 8 extend true Selected 719 atoms > graphics silhouettes false > isolde sim start #2/a > #1.2/A:86-87,89-91,96-110,173,175-180,183-187,208,245-248,278,281-288,290-291,297,300-302,305,334-337,371-374,376/a ISOLDE: started sim > select clear > isolde sim pause > select up 57 atoms, 60 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected atoms"" > isolde sim resume > ui mousemode right ""isolde tug atom"" > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select up 57 atoms, 60 bonds, 1 residue, 1 model selected > color :UNL orange > color byhetero > color :UNK orange > color byhetero > open C1CN(CCN1CCCN2C(=O)N3C=CC=CC3=N2)C4=CC(=CC=C4)Cl fromDatabase smiles Translated SMILES to 3D structure via NCI web service (SMILES: C1CN(CCN1CCCN2C(=O)N3C=CC=CC3=N2)C4=CC(=CC=C4)Cl) > setattr #3 res name TRZ Assigning name attribute to 1 item > select #3 48 atoms, 51 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected atoms"" > isolde ignore :UNK ISOLDE: currently ignoring 1 residues in model 1.2 ISOLDE: currently ignoring 1 residues in model 2 > hide :UNK ISOLDE: merge models Merging models #3 into #1.2. > hide #3 models > select up 48 atoms, 51 bonds, 1 residue, 1 model selected > show sel > select up 49 atoms, 52 bonds, 1 residue, 1 model selected > isolde parameterise sel Loading residue template for TRZ from internal database Residue name TRZ already corresponds to template MC_TRZ in the amber14 forcefield. If you wish to replace that template, re-run this command with override=True > isolde parameterise sel override true Running ANTECHAMBER command: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\TRISTA~1\AppData\Local\Temp\tmphr7vs6lu\ante.in.mol2 -fi mol2 -o C:\Users\TRISTA~1\AppData\Local\Temp\tmphr7vs6lu\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (TRZ) `` (TRZ) `Welcome to antechamber 20.0: molecular input file processor.` (TRZ) `` (TRZ) `Info: Finished reading file (C:\Users\TRISTA~1\AppData\Local\Temp\tmphr7vs6lu\ante.in.mol2); atoms read (49), bonds read (52).` (TRZ) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (TRZ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (TRZ) `bash.exe: warning: could not find /tmp, please create!` (TRZ) `` (TRZ) `` (TRZ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (TRZ) `bash.exe: warning: could not find /tmp, please create!` (TRZ) `Info: Total number of electrons: 196; net charge: 1` (TRZ) `` (TRZ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out` (TRZ) `bash.exe: warning: could not find /tmp, please create!` (TRZ) `` (TRZ) `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` (TRZ) `bash.exe: warning: could not find /tmp, please create!` (TRZ) `` (TRZ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (TRZ) `bash.exe: warning: could not find /tmp, please create!` (TRZ) `` Charges for residue TRZ determined OpenMM ffXML file TRZ written to the current working directory. New template added to forcefield as USER_TRZ. 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. > select zone sel 8 extend true Selected 854 atoms, 1 surfaces > isolde sim start #2/a > #1.2/*/A:90,96-103,105,108,173-187,189-190,202,204-205,208,220,243-251,272-275,277-288,297,301-302,305,310,312,329,333-337,340,372-373 > #3/* ISOLDE: started sim > select clear Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. [Repeated 1 time(s)] > select up 16 atoms, 15 bonds, 1 residue, 1 model selected > rd > show :UNK > isolde sim pause > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select up 49 atoms, 52 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected atoms"" > delete sel > select up 49 atoms, 52 bonds, 1 residue, 1 model selected > isolde parameterise sel override true Running ANTECHAMBER command: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\TRISTA~1\AppData\Local\Temp\tmpw4pcdxzi\ante.in.mol2 -fi mol2 -o C:\Users\TRISTA~1\AppData\Local\Temp\tmpw4pcdxzi\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (TRZ) `` (TRZ) `Welcome to antechamber 20.0: molecular input file processor.` (TRZ) `` (TRZ) `Info: Finished reading file (C:\Users\TRISTA~1\AppData\Local\Temp\tmpw4pcdxzi\ante.in.mol2); atoms read (49), bonds read (52).` (TRZ) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (TRZ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (TRZ) `bash.exe: warning: could not find /tmp, please create!` (TRZ) `` (TRZ) `` (TRZ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (TRZ) `bash.exe: warning: could not find /tmp, please create!` (TRZ) `Info: Total number of electrons: 196; net charge: 1` (TRZ) `` (TRZ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out` (TRZ) `bash.exe: warning: could not find /tmp, please create!` (TRZ) `` (TRZ) `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` (TRZ) `bash.exe: warning: could not find /tmp, please create!` (TRZ) `` (TRZ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (TRZ) `bash.exe: warning: could not find /tmp, please create!` (TRZ) `` Charges for residue TRZ determined OpenMM ffXML file TRZ written to the current working directory. New template added to forcefield as USER_TRZ. 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. > ui mousemode right ""bond rotation"" > torsion #1.2/?:1@N3,C7,C6,C5 38.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 38.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 64.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 64.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 62.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 62.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 15.50 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 15.50 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 20.50 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 20.50 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 43.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > ui mousemode right ""bond rotation"" > torsion #1.2/?:1@N3,C7,C6,C5 43.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 43.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > select zone sel 5 extend true Selected 349 atoms > isolde sim start #2/a > #1.2/*/A:100-101,103,176-178,185-186,245-247,278,281-282,285,287,335,372-373 > #3/* ISOLDE: started sim > torsion #1.2/?:1@N3,C7,C6,C5 43.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 43.00 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 69.62 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 70.91 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 64.88 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 54.49 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 65.97 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 89.13 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > ui mousemode right ""isolde tug atom"" > torsion #1.2/?:1@N3,C7,C6,C5 69.21 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 71.48 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 71.32 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 69.85 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > ui mousemode right ""isolde tug residue"" > ui mousemode right ""isolde tug atom"" > torsion #1.2/?:1@N3,C7,C6,C5 72.07 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 74.27 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 72.97 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 71.95 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > isolde sim pause > torsion #1.2/?:1@N3,C7,C6,C5 71.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 95.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > ui mousemode right ""isolde tug residue"" > ui mousemode right ""isolde tug atom"" > torsion #1.2/?:1@N3,C7,C6,C5 95.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 105.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 105.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 82.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 82.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 70.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 70.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 72.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 72.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 70.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 70.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 73.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > ui tool show Shell 0.01s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. > show #3 models > hide #3 models > torsion #1.2/?:1@N3,C7,C6,C5 73.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 73.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 73.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 74.46 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 74.46 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 77.46 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 77.46 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 66.46 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 66.46 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 71.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 71.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 75.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 75.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 86.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 86.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 86.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 86.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 83.46 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 83.46 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 81.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 81.96 Must specify exactly 4 atoms for 'torsion' command; you specified 8 > torsion #1.2/?:1@N3,C7,C6,C5 88.46 Must specify exactly 4 atoms for 'torsion' command; you specified 8 OpenGL version: 3.3.0 NVIDIA 529.08 OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_GB.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: HP Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC OS: Microsoft Windows 11 Pro (Build 22621) Memory: 34,007,068,672 MaxProcessMemory: 137,438,953,344 CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz OSLanguage: en-GB Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.13.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.7.22 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.12 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.2 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7rc202311140124 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.7rc1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.1 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.12 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-XMAS: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 comtypes: 1.1.14 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 et-xmlfile: 1.1.0 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.44.0 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.0 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 openpyxl: 3.1.2 openvr: 1.23.701 packaging: 23.2 pandas: 2.0.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.0.0 prompt-toolkit: 3.0.41 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynmrstar: 3.3.2 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.1 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 seaborn: 0.12.2 Send2Trash: 1.8.2 SEQCROW: 1.7.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.10 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1 }}} " defect closed normal General Controls fixed Eric Pettersen all ChimeraX