id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8883 Add Charges: Unknown class for change tracking: FakeAtom hegarpramastya@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.21996 ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open pdb:2WM4 format mmcif fromDatabase pdb 2wm4 title: X-ray structure of Mycobacterium tuberculosis cytochrome P450 CYP124 in complex with phytanic acid [more info...] Chain information for 2wm4 #1 --- Chain | Description | UniProt A | PUTATIVE CYTOCHROME P450 124 | CP124_MYCTU Non-standard residues in 2wm4 #1 --- CA — calcium ion HEM — protoporphyrin IX containing Fe (HEME) VGJ — (3R,7S,11S)-3,7,11,15-tetramethylhexadecanoic acid > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html > help help:devel > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html > color bychain > open 2bbv Summary of feedback from opening 2bbv fetched from pdb --- note | Fetching compressed mmCIF 2bbv from http://files.rcsb.org/download/2bbv.cif 2bbv title: The refined three-dimensional structure of an insect virus At 2.8 angstroms resolution [more info...] Chain information for 2bbv #2 --- Chain | Description | UniProt A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') | Non-standard residues in 2bbv #2 --- CA — calcium ion 2bbv mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > color bychain > open 2bbv 2bbv title: The refined three-dimensional structure of an insect virus At 2.8 angstroms resolution [more info...] Chain information for 2bbv #3 --- Chain | Description | UniProt A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') | Non-standard residues in 2bbv #3 --- CA — calcium ion 2bbv mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > color bychain > open 2bbv 2bbv title: The refined three-dimensional structure of an insect virus At 2.8 angstroms resolution [more info...] Chain information for 2bbv #4 --- Chain | Description | UniProt A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') | Non-standard residues in 2bbv #4 --- CA — calcium ion 2bbv mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > color bychain > open 2bbv 2bbv title: The refined three-dimensional structure of an insect virus At 2.8 angstroms resolution [more info...] Chain information for 2bbv #5 --- Chain | Description | UniProt A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') | Non-standard residues in 2bbv #5 --- CA — calcium ion 2bbv mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > color bychain > select add #1 3586 atoms, 3499 bonds, 9 pseudobonds, 603 residues, 2 models selected > hide #!2 target m > show #!2 models > show #!2 target m > open 2bbv 2bbv title: The refined three-dimensional structure of an insect virus At 2.8 angstroms resolution [more info...] Chain information for 2bbv #6 --- Chain | Description | UniProt A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') | Non-standard residues in 2bbv #6 --- CA — calcium ion 2bbv mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > view clip false [Repeated 1 time(s)] > lighting simple > style sel sphere Changed 3586 atom styles > style sel ball Changed 3586 atom styles > style sel stick Changed 3586 atom styles > style sel sphere Changed 3586 atom styles > show sel cartoons > hide sel cartoons [Repeated 1 time(s)] > show sel cartoons > 2wm4 Unknown command: 2wm4 > view sel > select subtract #1.1 3586 atoms, 3499 bonds, 603 residues, 1 model selected > select add #1 3586 atoms, 3499 bonds, 9 pseudobonds, 603 residues, 2 models selected > select add #2 11403 atoms, 11312 bonds, 26 pseudobonds, 1811 residues, 5 models selected > select subtract #1.1 11403 atoms, 11312 bonds, 17 pseudobonds, 1811 residues, 4 models selected > select add #1 11403 atoms, 11312 bonds, 26 pseudobonds, 1811 residues, 5 models selected > hide #!1 models > show #!1 models > select subtract #1 7817 atoms, 7813 bonds, 17 pseudobonds, 1208 residues, 3 models selected > select add #1.1 7817 atoms, 7813 bonds, 26 pseudobonds, 1208 residues, 4 models selected > help help:user > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html > palette list No custom palettes. 314 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6, Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, GnBu, GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8. > select 2bbv Expected an objects specifier or a keyword > select2bbv Unknown command: select2bbv > Incomplete command: sequence > Incomplete command: sequence > 2wm4 Unknown command: sequence 2wm4 > addcharge > addh ""#1/A #2/N,A,D,B,E,C,F #3/N,A,D,B,E,C,F #4/N,A,D,B,E,C,F > #5/N,A,D,B,E,C,F #6/N,A,D,B,E,C,F"" Summary of feedback from adding hydrogens to multiple structures --- warnings | Not adding hydrogens to 2wm4 #1/A GLU 59 CB because it is missing heavy-atom bond partners Not adding hydrogens to 2wm4 #1/A LYS 184 CB because it is missing heavy-atom bond partners Not adding hydrogens to 2wm4 #1/A GLN 188 CB because it is missing heavy-atom bond partners Not adding hydrogens to 2wm4 #1/A VAL 247 CB because it is missing heavy-atom bond partners Not adding hydrogens to 2wm4 #1/A ASP 248 CB because it is missing heavy-atom bond partners 10 messages similar to the above omitted notes | Termini for 2wm4 (#1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: 2wm4 #1/A LEU 3 Chain-final residues that are actual C termini: 2wm4 #1/A SER 428 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue 2wm4 #1/A SER 428 861 hydrogen bonds Adding 'H' to 2wm4 #1/A LEU 3 Termini for 2bbv (#2) chain N determined from SEQRES records Termini for 2bbv (#2) chain A determined from SEQRES records Termini for 2bbv (#2) chain D determined from SEQRES records Termini for 2bbv (#2) chain B determined from SEQRES records Termini for 2bbv (#2) chain E determined from SEQRES records 2 messages similar to the above omitted Chain-initial residues that are actual N termini: 2bbv #2/D ALA 364, 2bbv #2/E ALA 364, 2bbv #2/F ALA 364 Chain-initial residues that are not actual N termini: 2bbv #2/A LEU 56, 2bbv #2/B LEU 56, 2bbv #2/C THR 20, 2bbv #2/C ALA 55 Chain-final residues that are actual C termini: 2bbv #2/A ASN 363, 2bbv #2/B ASN 363, 2bbv #2/C ASN 363 Chain-final residues that are not actual C termini: 2bbv #2/D ALA 379, 2bbv #2/E ALA 379, 2bbv #2/C PRO 31, 2bbv #2/F ALA 379 973 hydrogen bonds Adding 'H' to 2bbv #2/A LEU 56 Adding 'H' to 2bbv #2/B LEU 56 Adding 'H' to 2bbv #2/C THR 20 Adding 'H' to 2bbv #2/C ALA 55 2bbv #2/D ALA 379 is not terminus, removing H atom from 'C' 2bbv #2/E ALA 379 is not terminus, removing H atom from 'C' 2bbv #2/F ALA 379 is not terminus, removing H atom from 'C' Termini for 2bbv (#3) chain N determined from SEQRES records Termini for 2bbv (#3) chain A determined from SEQRES records Termini for 2bbv (#3) chain D determined from SEQRES records Termini for 2bbv (#3) chain B determined from SEQRES records Termini for 2bbv (#3) chain E determined from SEQRES records 2 messages similar to the above omitted Chain-initial residues that are actual N termini: 2bbv #3/D ALA 364, 2bbv #3/E ALA 364, 2bbv #3/F ALA 364 Chain-initial residues that are not actual N termini: 2bbv #3/A LEU 56, 2bbv #3/B LEU 56, 2bbv #3/C THR 20, 2bbv #3/C ALA 55 Chain-final residues that are actual C termini: 2bbv #3/A ASN 363, 2bbv #3/B ASN 363, 2bbv #3/C ASN 363 Chain-final residues that are not actual C termini: 2bbv #3/D ALA 379, 2bbv #3/E ALA 379, 2bbv #3/C PRO 31, 2bbv #3/F ALA 379 973 hydrogen bonds Adding 'H' to 2bbv #3/A LEU 56 Adding 'H' to 2bbv #3/B LEU 56 Adding 'H' to 2bbv #3/C THR 20 Adding 'H' to 2bbv #3/C ALA 55 2bbv #3/D ALA 379 is not terminus, removing H atom from 'C' 2bbv #3/E ALA 379 is not terminus, removing H atom from 'C' 2bbv #3/F ALA 379 is not terminus, removing H atom from 'C' Termini for 2bbv (#4) chain N determined from SEQRES records Termini for 2bbv (#4) chain A determined from SEQRES records Termini for 2bbv (#4) chain D determined from SEQRES records Termini for 2bbv (#4) chain B determined from SEQRES records Termini for 2bbv (#4) chain E determined from SEQRES records 2 messages similar to the above omitted Chain-initial residues that are actual N termini: 2bbv #4/D ALA 364, 2bbv #4/E ALA 364, 2bbv #4/F ALA 364 Chain-initial residues that are not actual N termini: 2bbv #4/A LEU 56, 2bbv #4/B LEU 56, 2bbv #4/C THR 20, 2bbv #4/C ALA 55 Chain-final residues that are actual C termini: 2bbv #4/A ASN 363, 2bbv #4/B ASN 363, 2bbv #4/C ASN 363 Chain-final residues that are not actual C termini: 2bbv #4/D ALA 379, 2bbv #4/E ALA 379, 2bbv #4/C PRO 31, 2bbv #4/F ALA 379 973 hydrogen bonds Adding 'H' to 2bbv #4/A LEU 56 Adding 'H' to 2bbv #4/B LEU 56 Adding 'H' to 2bbv #4/C THR 20 Adding 'H' to 2bbv #4/C ALA 55 2bbv #4/D ALA 379 is not terminus, removing H atom from 'C' 2bbv #4/E ALA 379 is not terminus, removing H atom from 'C' 2bbv #4/F ALA 379 is not terminus, removing H atom from 'C' Termini for 2bbv (#5) chain N determined from SEQRES records Termini for 2bbv (#5) chain A determined from SEQRES records Termini for 2bbv (#5) chain D determined from SEQRES records Termini for 2bbv (#5) chain B determined from SEQRES records Termini for 2bbv (#5) chain E determined from SEQRES records 2 messages similar to the above omitted Chain-initial residues that are actual N termini: 2bbv #5/D ALA 364, 2bbv #5/E ALA 364, 2bbv #5/F ALA 364 Chain-initial residues that are not actual N termini: 2bbv #5/A LEU 56, 2bbv #5/B LEU 56, 2bbv #5/C THR 20, 2bbv #5/C ALA 55 Chain-final residues that are actual C termini: 2bbv #5/A ASN 363, 2bbv #5/B ASN 363, 2bbv #5/C ASN 363 Chain-final residues that are not actual C termini: 2bbv #5/D ALA 379, 2bbv #5/E ALA 379, 2bbv #5/C PRO 31, 2bbv #5/F ALA 379 973 hydrogen bonds Adding 'H' to 2bbv #5/A LEU 56 Adding 'H' to 2bbv #5/B LEU 56 Adding 'H' to 2bbv #5/C THR 20 Adding 'H' to 2bbv #5/C ALA 55 2bbv #5/D ALA 379 is not terminus, removing H atom from 'C' 2bbv #5/E ALA 379 is not terminus, removing H atom from 'C' 2bbv #5/F ALA 379 is not terminus, removing H atom from 'C' Termini for 2bbv (#6) chain N determined from SEQRES records Termini for 2bbv (#6) chain A determined from SEQRES records Termini for 2bbv (#6) chain D determined from SEQRES records Termini for 2bbv (#6) chain B determined from SEQRES records Termini for 2bbv (#6) chain E determined from SEQRES records 2 messages similar to the above omitted Chain-initial residues that are actual N termini: 2bbv #6/D ALA 364, 2bbv #6/E ALA 364, 2bbv #6/F ALA 364 Chain-initial residues that are not actual N termini: 2bbv #6/A LEU 56, 2bbv #6/B LEU 56, 2bbv #6/C THR 20, 2bbv #6/C ALA 55 Chain-final residues that are actual C termini: 2bbv #6/A ASN 363, 2bbv #6/B ASN 363, 2bbv #6/C ASN 363 Chain-final residues that are not actual C termini: 2bbv #6/D ALA 379, 2bbv #6/E ALA 379, 2bbv #6/C PRO 31, 2bbv #6/F ALA 379 973 hydrogen bonds Adding 'H' to 2bbv #6/A LEU 56 Adding 'H' to 2bbv #6/B LEU 56 Adding 'H' to 2bbv #6/C THR 20 Adding 'H' to 2bbv #6/C ALA 55 2bbv #6/D ALA 379 is not terminus, removing H atom from 'C' 2bbv #6/E ALA 379 is not terminus, removing H atom from 'C' 2bbv #6/F ALA 379 is not terminus, removing H atom from 'C' 42760 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue VGJ (net charge -1) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\Hegar\AppData\Local\Temp\tmppsdbz5x4\ante.in.mol2 -fi mol2 -o C:\Users\Hegar\AppData\Local\Temp\tmppsdbz5x4\ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n (VGJ) `` (VGJ) `Welcome to antechamber 20.0: molecular input file processor.` (VGJ) `` (VGJ) `Info: Finished reading file (C:\Users\Hegar\AppData\Local\Temp\tmppsdbz5x4\ante.in.mol2); atoms read (61), bonds read (60).` (VGJ) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (VGJ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (VGJ) `bash.exe: warning: could not find /tmp, please create!` (VGJ) `` (VGJ) `` (VGJ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (VGJ) `bash.exe: warning: could not find /tmp, please create!` (VGJ) `Info: Total number of electrons: 176; net charge: -1` (VGJ) `` (VGJ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out` (VGJ) `bash.exe: warning: could not find /tmp, please create!` (VGJ) `` (VGJ) `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` (VGJ) `bash.exe: warning: could not find /tmp, please create!` (VGJ) `` (VGJ) `Running: ""C:/Program Files/ChimeraX/bin/amber20/bin/atomtype"" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (VGJ) `bash.exe: warning: could not find /tmp, please create!` (VGJ) `` Charges for residue VGJ determined Assigning partial charges to residue CA (net charge +2) with am1-bcc method Assigning partial charges to residue HEM[FE] (net charge +2) with am1-bcc method Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 2118, in add_modified iterable_test = iter(modded) TypeError: 'FakeAtom' object is not iterable During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 319, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\cmd.py"", line 31, in cmd_addcharge add_charges(session, residues, method=method, status=session.logger.status, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 26, in add_charges add_nonstandard_res_charges(session, res_list, estimate_net_charge(res_list[0].atoms), File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\add_charge\charge.py"", line 305, in add_nonstandard_res_charges session.change_tracker.add_modified(a, ""charge changed"") File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 2120, in add_modified f(self._inst_to_int(modded), modded._c_pointer, reason.encode('utf-8')) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 2205, in _inst_to_int raise AssertionError(""Unknown class for change tracking: %s"" % inst.__class__.__name__) AssertionError: Unknown class for change tracking: FakeAtom AssertionError: Unknown class for change tracking: FakeAtom File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 2205, in _inst_to_int raise AssertionError(""Unknown class for change tracking: %s"" % inst.__class__.__name__) See log for complete Python traceback. OpenGL version: 3.3.13596 Core Profile Forward-Compatible Context 20.10.35.02 27.20.1034.6 OpenGL renderer: AMD Radeon HD 8500M Series OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: LENOVO Model: 20237 OS: Microsoft Windows 11 Education (Build 21996) Memory: 17,092,161,536 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i5-4200M CPU @ 2.50GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 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: 2022.6 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.11.0 }}} " defect closed normal Structure Editing duplicate all ChimeraX