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#8883 closed defect (duplicate)

Add Charges: Unknown class for change tracking: FakeAtom

Reported by:	hegarpramastya@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Structure Editing	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

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

Change History (2)

comment:1 by pett, 3 years ago

Component:	Unassigned → Structure Editing
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Reporter:	changed from hegarpramasty@… to hegarpramastya@…
Status:	new → accepted
Summary:	ChimeraX bug report submission → Add Charges: Unknown class for change tracking: FakeAtom

comment:2 by pett, 3 years ago

Resolution:	→ duplicate
Status:	accepted → closed

Hi Hegar,

Thanks for reporting this problem. It has been fixed in the ChimeraX 1.6 release candidate and daily build, so if you get either of those then you won't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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