id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4861 Failure running antechamber on Windows wenxiang.cao@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description coulombicUsing Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIC (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\myHP\AppData\Local\Temp\tmphr9qv0v0\ante.in.mol2 -fi mol2 -o C:\Users\myHP\AppData\Local\Temp\tmphr9qv0v0\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIC) (HIC) Welcome to antechamber 20.0: molecular input file processor. (HIC) (HIC) Info: Finished reading file (C:\Users\myHP\AppData\Local\Temp\tmphr9qv0v0\ante.in.mol2); atoms read (32), bonds read (32). (HIC) Info: Determining atomic numbers from atomic symbols which are case sensitive. (HIC) Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (HIC) /usr/bin/antechamber: Fatal Error! (HIC) Cannot properly run ""C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac"". (HIC) No such file or directory Failure running ANTECHAMBER for residue HIC Check reply log for details Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""D:\user\Box Sync\manuscripts\Dorit lab yeat WT and 167 mutant > cryoEM\actin structure files Niels Volkmann shared on 21-01-19\wt_model.pdb"" > format pdb Summary of feedback from opening D:\user\Box Sync\manuscripts\Dorit lab yeat WT and 167 mutant cryoEM\actin structure files Niels Volkmann shared on 21-01-19\wt_model.pdb --- warnings | Ignored bad PDB record found on line 25 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 26 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 27 BOND : 0.006 0.054 14780 Ignored bad PDB record found on line 28 ANGLE : 0.947 15.272 20050 Ignored bad PDB record found on line 29 CHIRALITY : 0.057 0.244 2230 16 messages similar to the above omitted Chain information for wt_model.pdb #1 --- Chain | Description A B C D E | No description available > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A GLN 41 /A MET 47 /A GLN 49 /A LYS 50 /A ASP 51 /A PHE 375 /B GLN 41 /B MET 47 /B GLN 49 /B LYS 50 /B ASP 51 /B PHE 375 /C GLN 41 /C MET 47 /C GLN 49 /C LYS 50 /C ASP 51 /C PHE 375 /D GLN 41 /D MET 47 /D GLN 49 /D LYS 50 /D ASP 51 /D PHE 375 /E GLN 41 /E MET 47 /E GLN 49 /E LYS 50 /E ASP 51 /E PHE 375 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for wt_model.pdb_A SES surface #1.1: minimum, -17.47, mean -2.40, maximum 12.76 Coulombic values for wt_model.pdb_B SES surface #1.2: minimum, -17.27, mean -2.41, maximum 12.49 Coulombic values for wt_model.pdb_C SES surface #1.3: minimum, -17.02, mean -2.42, maximum 12.37 Coulombic values for wt_model.pdb_D SES surface #1.4: minimum, -17.84, mean -2.43, maximum 12.57 Coulombic values for wt_model.pdb_E SES surface #1.5: minimum, -17.67, mean -2.42, maximum 13.30 To also show corresponding color key, enter the above coulombic command and add key true > close > open 3mfp format mmcif fromDatabase pdb 3mfp title: Atomic model of F-actin based on a 6.6 angstrom resolution cryoEM map [more info...] Chain information for 3mfp #1 --- Chain | Description A | Actin, α skeletal muscle Non-standard residues in 3mfp #1 --- ADP — adenosine-5'-diphosphate 3mfp mmCIF Assemblies --- 1| representative helical assembly 2| helical asymmetric unit 3| helical asymmetric unit, std helical frame > coulombic Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIC (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\myHP\AppData\Local\Temp\tmp4l_jhnpw\ante.in.mol2 -fi mol2 -o C:\Users\myHP\AppData\Local\Temp\tmp4l_jhnpw\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIC) `` (HIC) `Welcome to antechamber 20.0: molecular input file processor.` (HIC) `` (HIC) `Info: Finished reading file (C:\Users\myHP\AppData\Local\Temp\tmp4l_jhnpw\ante.in.mol2); atoms read (32), bonds read (32).` (HIC) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIC) `Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIC) `/usr/bin/antechamber: Fatal Error!` (HIC) `Cannot properly run ""C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac"".` (HIC) `No such file or directory` Failure running ANTECHAMBER for residue HIC Check reply log for details > select hic Expected an objects specifier or a keyword > help help:user > help help:user > close > open 3d6y Summary of feedback from opening 3d6y fetched from pdb --- notes | Fetching compressed mmCIF 3d6y from http://files.rcsb.org/download/3d6y.cif Fetching CCD BER from http://ligand-expo.rcsb.org/reports/B/BER/BER.cif Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif 3d6y title: Crystal structure of R275E mutant of BMRR bound to DNA and berberine [more info...] Chain information for 3d6y #1 --- Chain | Description A | Multidrug-efflux transporter 1 regulator B | BMR promoter DNA Non-standard residues in 3d6y #1 --- BER — berberine GOL — glycerol (glycerin; propane-1,2,3-triol) 3d6y mmCIF Assemblies --- 1| author_and_software_defined_assembly > select :BER 25 atoms, 29 bonds, 1 residue, 1 model selected > select :GOL 12 atoms, 10 bonds, 2 residues, 1 model selected > select :GOL 12 atoms, 10 bonds, 2 residues, 1 model selected > select clear > select :GOL 12 atoms, 10 bonds, 2 residues, 1 model selected > select :BER 25 atoms, 29 bonds, 1 residue, 1 model selected > select :GOL 12 atoms, 10 bonds, 2 residues, 1 model selected > close > open 3d6y fromDatabase rcsb_bio maxAssemblies 1 Summary of feedback from opening 3d6y fetched from rcsb_bio --- note | Fetching compressed 3d6y bioassembly 1 from https://files.rcsb.org/download/3d6y.pdb1.gz subunit 1 title: Crystal structure of R275E mutant of BMRR bound to DNA and berberine [more info...] Chain information for subunit 1 #1.1 --- Chain | Description A | No description available B | No description available Non-standard residues in subunit 1 #1.1 --- BER — berberine GOL — glycerol (glycerin; propane-1,2,3-triol) Chain information for subunit 2 #1.2 --- Chain | Description A | No description available B | No description available Opened 1 biological assemblies for 3d6y > hide #1.2 models > show #1.2 models > hide #1.1 models > show #1.1 models > hide #1.2 models > show #1.2 models > select :GOL 24 atoms, 20 bonds, 4 residues, 2 models selected > select :GOL 24 atoms, 20 bonds, 4 residues, 2 models selected > select :GOL 24 atoms, 20 bonds, 4 residues, 2 models selected > select :BER 50 atoms, 58 bonds, 2 residues, 2 models selected > select :GOL 24 atoms, 20 bonds, 4 residues, 2 models selected > select :BER 50 atoms, 58 bonds, 2 residues, 2 models selected > hide :gol > hide solvent > hide protein > ~hide protein Unknown command: ~hide protein > show protein > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > hide protein > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > select clear > hide protein > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > hide protein > select clear > coulombic Using Amber 20 recommended default charges and atom types for standard residues Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for subunit 1_A SES surface #1.1.1: minimum, -16.84, mean -2.11, maximum 14.59 Coulombic values for subunit 1_B SES surface #1.1.2: minimum, -18.71, mean -10.15, maximum -1.37 Coulombic values for subunit 2_A SES surface #1.2.1: minimum, -16.09, mean -1.98, maximum 15.15 Coulombic values for subunit 2_B SES surface #1.2.2: minimum, -18.78, mean -10.16, maximum -1.36 To also show corresponding color key, enter the above coulombic command and add key true > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > hide :gol > hide solvent > hide protein > coulombic protein range -10,10 Coulombic values for subunit 1_A SES surface #1.1.1: minimum, -16.84, mean -2.11, maximum 14.59 Coulombic values for subunit 2_A SES surface #1.2.1: minimum, -16.09, mean -1.98, maximum 15.15 > close > open 3mfp format mmcif fromDatabase pdb 3mfp title: Atomic model of F-actin based on a 6.6 angstrom resolution cryoEM map [more info...] Chain information for 3mfp #1 --- Chain | Description A | Actin, α skeletal muscle Non-standard residues in 3mfp #1 --- ADP — adenosine-5'-diphosphate 3mfp mmCIF Assemblies --- 1| representative helical assembly 2| helical asymmetric unit 3| helical asymmetric unit, std helical frame > hide :ADP > hide solvent > hide protein > select clear > coulombic protein range -10,10 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIC (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\myHP\AppData\Local\Temp\tmptnc6ju7l\ante.in.mol2 -fi mol2 -o C:\Users\myHP\AppData\Local\Temp\tmptnc6ju7l\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIC) `` (HIC) `Welcome to antechamber 20.0: molecular input file processor.` (HIC) `` (HIC) `Info: Finished reading file (C:\Users\myHP\AppData\Local\Temp\tmptnc6ju7l\ante.in.mol2); atoms read (32), bonds read (32).` (HIC) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIC) `Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIC) `/usr/bin/antechamber: Fatal Error!` (HIC) `Cannot properly run ""C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac"".` (HIC) `No such file or directory` Failure running ANTECHAMBER for residue HIC Check reply log for details > select :hic 11 atoms, 11 bonds, 1 residue, 1 model selected Alignment identifier is 1/A > select :his 80 atoms, 81 bonds, 8 residues, 1 model selected > select clear > select clear > select :his 80 atoms, 81 bonds, 8 residues, 1 model selected > ui tool show ""Build Structure"" > ui tool show Updates > toolshed show > help help:devel > help help:index.html > rename #1 mutant4 > build modify :hic name his Missing or invalid ""atom"" argument: Must specify exactly one atom (specified 11) > select clear > select :hic 11 atoms, 11 bonds, 1 residue, 1 model selected > swapaa sel :his Using Dunbrack library /A HIC 73: phi -109.1, psi 24.1 trans Dunbrack rotamer library does not support :HIS > ui tool show ""Command Line Interface"" > ui tool show Log > select :h Nothing selected > select :his 80 atoms, 81 bonds, 8 residues, 1 model selected > select :hic 11 atoms, 11 bonds, 1 residue, 1 model selected > style sel ball Changed 11 atom styles > show sel > color sel byhetero > select clear > coulombic Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIC (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\myHP\AppData\Local\Temp\tmpbo0puy45\ante.in.mol2 -fi mol2 -o C:\Users\myHP\AppData\Local\Temp\tmpbo0puy45\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIC) `` (HIC) `Welcome to antechamber 20.0: molecular input file processor.` (HIC) `` (HIC) `Info: Finished reading file (C:\Users\myHP\AppData\Local\Temp\tmpbo0puy45\ante.in.mol2); atoms read (32), bonds read (32).` (HIC) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIC) `Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIC) `/usr/bin/antechamber: Fatal Error!` (HIC) `Cannot properly run ""C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac"".` (HIC) `No such file or directory` Failure running ANTECHAMBER for residue HIC Check reply log for details > select hic Expected an objects specifier or a keyword > select :hic 11 atoms, 11 bonds, 1 residue, 1 model selected > coulombic :hic range -10,10 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIC (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\myHP\AppData\Local\Temp\tmpxvxquhmd\ante.in.mol2 -fi mol2 -o C:\Users\myHP\AppData\Local\Temp\tmpxvxquhmd\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIC) `` (HIC) `Welcome to antechamber 20.0: molecular input file processor.` (HIC) `` (HIC) `Info: Finished reading file (C:\Users\myHP\AppData\Local\Temp\tmpxvxquhmd\ante.in.mol2); atoms read (32), bonds read (32).` (HIC) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIC) `Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIC) `/usr/bin/antechamber: Fatal Error!` (HIC) `Cannot properly run ""C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac"".` (HIC) `No such file or directory` Failure running ANTECHAMBER for residue HIC Check reply log for details > hide sel > select clear > coulombic protein range -10,10 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIC (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\myHP\AppData\Local\Temp\tmp8t49fojj\ante.in.mol2 -fi mol2 -o C:\Users\myHP\AppData\Local\Temp\tmp8t49fojj\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIC) `` (HIC) `Welcome to antechamber 20.0: molecular input file processor.` (HIC) `` (HIC) `Info: Finished reading file (C:\Users\myHP\AppData\Local\Temp\tmp8t49fojj\ante.in.mol2); atoms read (32), bonds read (32).` (HIC) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIC) `Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIC) `/usr/bin/antechamber: Fatal Error!` (HIC) `Cannot properly run ""C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac"".` (HIC) `No such file or directory` Failure running ANTECHAMBER for residue HIC Check reply log for details > coulombic protein range -10,10 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIC (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\myHP\AppData\Local\Temp\tmp9teu92i_\ante.in.mol2 -fi mol2 -o C:\Users\myHP\AppData\Local\Temp\tmp9teu92i_\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIC) `` (HIC) `Welcome to antechamber 20.0: molecular input file processor.` (HIC) `` (HIC) `Info: Finished reading file (C:\Users\myHP\AppData\Local\Temp\tmp9teu92i_\ante.in.mol2); atoms read (32), bonds read (32).` (HIC) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIC) `Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIC) `/usr/bin/antechamber: Fatal Error!` (HIC) `Cannot properly run ""C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac"".` (HIC) `No such file or directory` Failure running ANTECHAMBER for residue HIC Check reply log for details > coulombic :1-72, 74-375 range -10,10 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIC (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\myHP\AppData\Local\Temp\tmp53jgcy2f\ante.in.mol2 -fi mol2 -o C:\Users\myHP\AppData\Local\Temp\tmp53jgcy2f\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIC) `` (HIC) `Welcome to antechamber 20.0: molecular input file processor.` (HIC) `` (HIC) `Info: Finished reading file (C:\Users\myHP\AppData\Local\Temp\tmp53jgcy2f\ante.in.mol2); atoms read (32), bonds read (32).` (HIC) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIC) `Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIC) `/usr/bin/antechamber: Fatal Error!` (HIC) `Cannot properly run ""C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac"".` (HIC) `No such file or directory` Failure running ANTECHAMBER for residue HIC Check reply log for details > delete :hic > coulombic protein range -10,10 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for mutant4_A SES surface #1.2: minimum, -18.10, mean -2.62, maximum 10.75 > select :6110 Nothing selected > select :61 9 atoms, 8 bonds, 1 residue, 1 model selected > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > close > open 3mfp format mmcif fromDatabase pdb 3mfp title: Atomic model of F-actin based on a 6.6 angstrom resolution cryoEM map [more info...] Chain information for 3mfp #1 --- Chain | Description A | Actin, α skeletal muscle Non-standard residues in 3mfp #1 --- ADP — adenosine-5'-diphosphate 3mfp mmCIF Assemblies --- 1| representative helical assembly 2| helical asymmetric unit 3| helical asymmetric unit, std helical frame > color bynucleotide > color bynucleotide Alignment identifier is 1/A > surface > coulombic Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIC (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\myHP\AppData\Local\Temp\tmphr9qv0v0\ante.in.mol2 -fi mol2 -o C:\Users\myHP\AppData\Local\Temp\tmphr9qv0v0\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (HIC) `` (HIC) `Welcome to antechamber 20.0: molecular input file processor.` (HIC) `` (HIC) `Info: Finished reading file (C:\Users\myHP\AppData\Local\Temp\tmphr9qv0v0\ante.in.mol2); atoms read (32), bonds read (32).` (HIC) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIC) `Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIC) `/usr/bin/antechamber: Fatal Error!` (HIC) `Cannot properly run ""C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac"".` (HIC) `No such file or directory` Failure running ANTECHAMBER for residue HIC Check reply log for details > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. OpenGL version: 3.3.14739 Core Profile Forward-Compatible Context 21.6.1 27.20.22001.14011 OpenGL renderer: AMD Radeon(TM) RX Vega 10 Graphics OpenGL vendor: ATI Technologies Inc. Manufacturer: HP Model: HP Laptop 17-ca1xxx OS: Microsoft Windows 10 Home (Build 19042) Memory: 14,942,511,104 MaxProcessMemory: 137,438,953,344 CPU: 8 AMD Ryzen 7 3700U with Radeon Vega Mobile Gfx OSLanguage: en-US Locale: ('en_US', 'cp936') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 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: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 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: 2.0.1 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: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 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: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 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: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 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 pywin32: 228 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 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 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 WMI: 1.5.1 File attachment: antechanber error.PNG }}} [attachment:""antechanber error.PNG""] " defect closed normal Structure Editing fixed chimera-programmers all ChimeraX