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#8300 closed defect (limitation)

Didn't find section 'Peptide bond' in tab 'ISOLDE'

Reported by:	stjiafle@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:	Greg Couch
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
it was a sel #1/c-h command

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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 C:\Users\yayin\Downloads\7ugu.pdb format pdb

7ugu.pdb title:  
Structure of enolase from streptococcus pyogenes [more info...]  
  
Chain information for 7ugu.pdb #1  
---  
Chain | Description | UniProt  
A B C D E F G H | enolase | A3F8V6_STRPY  
  

> select #1/a,b

13188 atoms, 13294 bonds, 872 residues, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> toolshed show

Downloading bundle SEQCROW-1.5.10-py3-none-any.whl  
[Repeated 1 time(s)]

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3.1  
[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip
install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\yayin\downloads\seqcrow-1.5.10-py3-none-any.whl  
Requirement already satisfied: scipy in c:\program
files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.10) (1.9.0)  
Requirement already satisfied: ChimeraX-Core<=1.6,>=1.2 in c:\program
files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.10) (1.5)  
Requirement already satisfied: psutil in c:\program
files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.10) (5.9.1)  
Requirement already satisfied: jinja2 in c:\program
files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.10) (3.1.2)  
Collecting Send2Trash  
Using cached Send2Trash-1.8.0-py3-none-any.whl (18 kB)  
Requirement already satisfied: MarkupSafe>=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from jinja2->SEQCROW==1.5.10) (2.1.1)  
Requirement already satisfied: numpy<1.25.0,>=1.18.5 in c:\program
files\chimerax\bin\lib\site-packages (from scipy->SEQCROW==1.5.10) (1.23.1)  
Installing collected packages: Send2Trash, SEQCROW  
Successfully installed SEQCROW-1.5.10 Send2Trash-1.8.0  
\---  

Successfully installed SEQCROW-1.5.10 Send2Trash-1.8.0  
Installed SEQCROW (1.5.10)  
Downloading bundle ChimeraX_StrudelScore-0.2-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3.1  
[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip
install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\yayin\downloads\chimerax_strudelscore-0.2-py3-none-any.whl  
Collecting ChimeraX-Clipper>=0.15.0  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.19.0/ChimeraX_Clipper-0.19.0-cp39-cp39-win_amd64.whl
(7.4 MB)  
\---------------------------------------- 7.4/7.4 MB 4.0 MB/s eta 0:00:00  
Collecting biopython>=1.77  
Downloading biopython-1.80-cp39-cp39-win_amd64.whl (2.7 MB)  
\---------------------------------------- 2.7/2.7 MB 10.8 MB/s eta 0:00:00  
Collecting ChimeraX-ISOLDE>=1.2  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxisolde/releases/1.5/ChimeraX_ISOLDE-1.5-cp39-cp39-win_amd64.whl
(90.9 MB)  
\---------------------------------------- 90.9/90.9 MB 6.9 MB/s eta 0:00:00  
Collecting pandas>=0.24  
Downloading pandas-1.5.2-cp39-cp39-win_amd64.whl (10.9 MB)  
\--------------------------------------- 10.9/10.9 MB 11.1 MB/s eta 0:00:00  
Requirement already satisfied: ChimeraX-Core<1.6 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-StrudelScore==0.2) (1.5)  
Collecting mrcfile>=1.1  
Downloading mrcfile-1.4.3-py2.py3-none-any.whl (43 kB)  
\---------------------------------------- 43.9/43.9 kB ? eta 0:00:00  
Collecting threed-strudel>0.9  
Downloading threed_strudel-0.9.18-py3-none-any.whl (7.1 MB)  
\---------------------------------------- 7.1/7.1 MB 12.2 MB/s eta 0:00:00  
Collecting recordtype>=1.3  
Downloading recordtype-1.4-py2.py3-none-any.whl (13 kB)  
Requirement already satisfied: numpy in c:\program
files\chimerax\bin\lib\site-packages (from biopython>=1.77->ChimeraX-
StrudelScore==0.2) (1.23.1)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=8.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Clipper>=0.15.0->ChimeraX-
StrudelScore==0.2) (8.0.3)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Clipper>=0.15.0->ChimeraX-
StrudelScore==0.2) (1.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.36 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Clipper>=0.15.0->ChimeraX-
StrudelScore==0.2) (1.41.5)  
Requirement already satisfied: pytz>=2020.1 in c:\program
files\chimerax\bin\lib\site-packages (from pandas>=0.24->ChimeraX-
StrudelScore==0.2) (2022.6)  
Requirement already satisfied: python-dateutil>=2.8.1 in c:\program
files\chimerax\bin\lib\site-packages (from pandas>=0.24->ChimeraX-
StrudelScore==0.2) (2.8.2)  
Requirement already satisfied: six in c:\program files\chimerax\bin\lib\site-
packages (from recordtype>=1.3->ChimeraX-StrudelScore==0.2) (1.16.0)  
Requirement already satisfied: scipy in c:\program
files\chimerax\bin\lib\site-packages (from threed-strudel>0.9->ChimeraX-
StrudelScore==0.2) (1.9.0)  
Requirement already satisfied: psutil in c:\program
files\chimerax\bin\lib\site-packages (from threed-strudel>0.9->ChimeraX-
StrudelScore==0.2) (5.9.1)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (2.0.1)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (1.0.2)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (2.0.3)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (1.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (2.6.8)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (2.8)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (1.2)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (1.5.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (1.9.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (1.2.2)  
Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-
StrudelScore==0.2) (1.24.3)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-
StrudelScore==0.2) (1.0)  
Requirement already satisfied: ChimeraX-IO~=1.0.1 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PDB~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (1.0.1)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-
StrudelScore==0.2) (1.10)  
Requirement already satisfied: ChimeraX-Map~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-
StrudelScore==0.2) (1.1.2)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-
StrudelScore==0.2) (2.0)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-
StrudelScore==0.2) (1.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-
StrudelScore==0.2) (1.1.1)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (2.1.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (2.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (1.0.1)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (2.0)  
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper>=0.15.0->ChimeraX-StrudelScore==0.2) (1.3)  
Installing collected packages: recordtype, mrcfile, biopython, threed-strudel,
pandas, ChimeraX-Clipper, ChimeraX-ISOLDE, ChimeraX-StrudelScore  
Successfully installed ChimeraX-Clipper-0.19.0 ChimeraX-ISOLDE-1.5 ChimeraX-
StrudelScore-0.2 biopython-1.80 mrcfile-1.4.3 pandas-1.5.2 recordtype-1.4
threed-strudel-0.9.18  
\---  

Successfully installed ChimeraX-Clipper-0.19.0 ChimeraX-ISOLDE-1.5 ChimeraX-
StrudelScore-0.2 biopython-1.80 mrcfile-1.4.3 pandas-1.5.2 recordtype-1.4
threed-strudel-0.9.18  
Installed ChimeraX-Clipper (0.19.0)  
Installed ChimeraX-ISOLDE (1.5)  
Installed ChimeraX-StrudelScore (0.2)  
Downloading bundle ChimeraX_RMF-0.11-cp39-cp39-win_amd64.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3.1  
[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip
install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\yayin\downloads\chimerax_rmf-0.11-cp39-cp39-win_amd64.whl  
Requirement already satisfied: ChimeraX-Core>=1.3 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-RMF==0.11) (1.5)  
Requirement already satisfied: ChimeraX-Atomic>=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-RMF==0.11) (1.41.5)  
Requirement already satisfied: ChimeraX-UI>=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-RMF==0.11) (1.24.3)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (2.0.3)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (1.0)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=8.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (8.0.3)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (1.0.2)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (2.6.8)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (2.0.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (1.2)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (2.8)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (1.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI>=1.0->ChimeraX-
RMF==0.11) (1.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI>=1.0->ChimeraX-
RMF==0.11) (1.1.1)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-RMF==0.11) (1.5.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-RMF==0.11) (1.9.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-RMF==0.11) (1.2.2)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-RMF==0.11) (1.0)  
Requirement already satisfied: ChimeraX-IO~=1.0.1 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PDB~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-RMF==0.11) (1.0.1)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI>=1.0->ChimeraX-RMF==0.11) (1.0.1)  
Requirement already satisfied: ChimeraX-Map~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-RMF==0.11) (1.1.2)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-RMF==0.11) (2.0)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-RMF==0.11) (1.10)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (2.1.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
RMF==0.11) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-RMF==0.11) (2.0)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-RMF==0.11) (2.0)  
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-RMF==0.11) (1.3)  
Installing collected packages: ChimeraX-RMF  
Successfully installed ChimeraX-RMF-0.11  
\---  

Successfully installed ChimeraX-RMF-0.11  
Installed ChimeraX-RMF (0.11)  
Downloading bundle ChimeraX_XMAS-1.1.2-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3.1  
[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip
install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\yayin\downloads\chimerax_xmas-1.1.2-py3-none-any.whl  
Collecting seaborn  
Downloading seaborn-0.12.2-py3-none-any.whl (293 kB)  
\-------------------------------------- 293.3/293.3 kB 4.5 MB/s eta 0:00:00  
Collecting openpyxl  
Downloading openpyxl-3.0.10-py2.py3-none-any.whl (242 kB)  
\-------------------------------------- 242.1/242.1 kB 7.5 MB/s eta 0:00:00  
Collecting qtrangeslider  
Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB)  
Requirement already satisfied: ChimeraX-Core~=1.3 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-XMAS==1.1.2) (1.5)  
Requirement already satisfied: pandas in
c:\users\yayin\appdata\local\ucsf\chimerax\1.5\site-packages (from ChimeraX-
XMAS==1.1.2) (1.5.2)  
Requirement already satisfied: ChimeraX-UI~=1.3 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-XMAS==1.1.2) (1.24.3)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.2) (1.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.2) (1.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.2) (1.1.1)  
Collecting et-xmlfile  
Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)  
Requirement already satisfied: python-dateutil>=2.8.1 in c:\program
files\chimerax\bin\lib\site-packages (from pandas->ChimeraX-XMAS==1.1.2)
(2.8.2)  
Requirement already satisfied: pytz>=2020.1 in c:\program
files\chimerax\bin\lib\site-packages (from pandas->ChimeraX-XMAS==1.1.2)
(2022.6)  
Requirement already satisfied: numpy>=1.20.3 in c:\program
files\chimerax\bin\lib\site-packages (from pandas->ChimeraX-XMAS==1.1.2)
(1.23.1)  
Requirement already satisfied: matplotlib!=3.6.1,>=3.1 in c:\program
files\chimerax\bin\lib\site-packages (from seaborn->ChimeraX-XMAS==1.1.2)
(3.5.2)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-
UI~=1.3->ChimeraX-XMAS==1.1.2) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-
UI~=1.3->ChimeraX-XMAS==1.1.2) (1.2)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.0.1)  
Requirement already satisfied: pyparsing>=2.2.1 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (3.0.9)  
Requirement already satisfied: fonttools>=4.22.0 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (4.38.0)  
Requirement already satisfied: cycler>=0.10 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (0.11.0)  
Requirement already satisfied: pillow>=6.2.0 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (9.2.0)  
Requirement already satisfied: packaging>=20.0 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (21.3)  
Requirement already satisfied: kiwisolver>=1.0.1 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (1.4.4)  
Requirement already satisfied: six>=1.5 in c:\program
files\chimerax\bin\lib\site-packages (from python-
dateutil>=2.8.1->pandas->ChimeraX-XMAS==1.1.2) (1.16.0)  
Installing collected packages: qtrangeslider, et-xmlfile, openpyxl, seaborn,
ChimeraX-XMAS  
Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.0.10
qtrangeslider-0.1.5 seaborn-0.12.2  
\---  

Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.0.10
qtrangeslider-0.1.5 seaborn-0.12.2  
Installed ChimeraX-XMAS (1.1.2)  
Downloading bundle ChimeraX_Phenix-0.3-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3.1  
[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip
install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\yayin\downloads\chimerax_phenix-0.3-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Atomic>=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Phenix==0.3) (1.41.5)  
Requirement already satisfied: ChimeraX-Core>=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Phenix==0.3) (1.5)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.2)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.8)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.0.3)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.0.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.6.8)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.0.2)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.1)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=8.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (8.0.3)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.0)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.5.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.9.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.2.2)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0)  
Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.24.3)  
Requirement already satisfied: ChimeraX-IO~=1.0.1 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PDB~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0.1)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.10)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.1.2)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.1.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.1.1)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0.1)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.3)  
Installing collected packages: ChimeraX-Phenix  
Successfully installed ChimeraX-Phenix-0.3  
\---  

Successfully installed ChimeraX-Phenix-0.3  
Installed ChimeraX-Phenix (0.3)  
Downloading bundle ChimeraX_PhenixUI-1.0.5-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3.1  
[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip
install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\yayin\downloads\chimerax_phenixui-1.0.5-py3-none-any.whl  
Requirement already satisfied: ChimeraX-UI~=1.21 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PhenixUI==1.0.5) (1.24.3)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PhenixUI==1.0.5) (2.0)  
Requirement already satisfied: ChimeraX-CheckWaters~=1.3 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PhenixUI==1.0.5) (1.3)  
Requirement already satisfied: ChimeraX-PDB~=2.6 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PhenixUI==1.0.5) (2.6.8)  
Requirement already satisfied: ChimeraX-Atomic~=1.32 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PhenixUI==1.0.5) (1.41.5)  
Requirement already satisfied: ChimeraX-Core~=1.5dev1 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PhenixUI==1.0.5) (1.5)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.32->ChimeraX-
PhenixUI==1.0.5) (1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.32->ChimeraX-
PhenixUI==1.0.5) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.32->ChimeraX-
PhenixUI==1.0.5) (1.2)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.32->ChimeraX-
PhenixUI==1.0.5) (2.0.3)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.32->ChimeraX-
PhenixUI==1.0.5) (2.0.1)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.32->ChimeraX-
PhenixUI==1.0.5) (2.8)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.32->ChimeraX-
PhenixUI==1.0.5) (1.0.2)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=8.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.32->ChimeraX-
PhenixUI==1.0.5) (8.0.3)  
Requirement already satisfied: ChimeraX-HBonds~=2.3 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
CheckWaters~=1.3->ChimeraX-PhenixUI==1.0.5) (2.4)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-MapData~=2.0->ChimeraX-
PhenixUI==1.0.5) (1.2.2)  
Requirement already satisfied: ChimeraX-IO~=1.0.1 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PDB~=2.6->ChimeraX-
PhenixUI==1.0.5) (1.0.1)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PDB~=2.6->ChimeraX-
PhenixUI==1.0.5) (1.5.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-PDB~=2.6->ChimeraX-
PhenixUI==1.0.5) (1.9.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.21->ChimeraX-
PhenixUI==1.0.5) (1.1.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI~=1.21->ChimeraX-
PhenixUI==1.0.5) (1.0)  
Requirement already satisfied: ChimeraX-AtomSearch~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-HBonds~=2.3->ChimeraX-
CheckWaters~=1.3->ChimeraX-PhenixUI==1.0.5) (2.0.1)  
Requirement already satisfied: ChimeraX-ChemGroup~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-HBonds~=2.3->ChimeraX-
CheckWaters~=1.3->ChimeraX-PhenixUI==1.0.5) (2.0)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.0.5) (1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.21->ChimeraX-PhenixUI==1.0.5) (1.0.1)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.0.5) (1.10)  
Requirement already satisfied: ChimeraX-Map~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.0.5) (1.1.2)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.32->ChimeraX-
PhenixUI==1.0.5) (2.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.32->ChimeraX-
PhenixUI==1.0.5) (2.1.1)  
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.32->ChimeraX-PhenixUI==1.0.5) (1.3)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.32->ChimeraX-PhenixUI==1.0.5) (2.0)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.32->ChimeraX-PhenixUI==1.0.5) (2.0)  
Installing collected packages: ChimeraX-PhenixUI  
Successfully installed ChimeraX-PhenixUI-1.0.5  
\---  

Successfully installed ChimeraX-PhenixUI-1.0.5  
Installed ChimeraX-PhenixUI (1.0.5)  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select #1/a,b

Missing required "contacting" argument  

> interfaces select #1/a,b

Missing required "contacting" argument  

> interfaces select & ~solvent #1/a,b

Missing or invalid "atoms" argument: invalid atoms specifier  

> select c-h

Expected an objects specifier or a keyword  

> select #1/c-h

39564 atoms, 39882 bonds, 2616 residues, 1 model selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\yayin\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\toolbar.py", line 299, in _selection_changed_cb  
self._enable_if_single_peptide_selected_cb()  
File "C:\Users\yayin\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\toolbar.py", line 285, in
_enable_if_single_peptide_selected_cb  
self.set_enabled(key, enable)  
File "C:\Users\yayin\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\isolde\toolbar.py", line 113, in set_enabled  
self.session.toolbar.set_enabled(enabled, tab, section, display_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\manager.py", line 164, in set_enabled  
tb.set_enabled(enabled, tab_title, section_title, button_title)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 246, in set_enabled  
self.ttb.set_enabled(enabled, tab_title, section_title, button_title)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\tabbedtoolbar.py", line 496, in set_enabled  
raise ValueError(f"Didn't find section '{section_title}' in tab
'{tab_title}'")  
ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE'  
  
Error processing trigger "selection changed":  
ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\tabbedtoolbar.py", line 496, in set_enabled  
raise ValueError(f"Didn't find section '{section_title}' in tab
'{tab_title}'")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8853
OpenGL renderer: Intel(R) Iris(R) Plus Graphics
OpenGL vendor: Intel

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: SAMSUNG ELECTRONICS CO., LTD.
Model: 950QCG
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 12,635,295,744
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz
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
    biopython: 1.80
    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-Clipper: 0.19.0
    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-ISOLDE: 1.5
    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-Phenix: 0.3
    ChimeraX-PhenixUI: 1.0.5
    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-RMF: 0.11
    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-StrudelScore: 0.2
    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-XMAS: 1.1.2
    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
    et-xmlfile: 1.1.0
    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
    mrcfile: 1.4.3
    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
    openpyxl: 3.0.10
    openvr: 1.23.701
    packaging: 21.3
    pandas: 1.5.2
    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
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    recordtype: 1.4
    requests: 2.28.1
    scipy: 1.9.0
    seaborn: 0.12.2
    Send2Trash: 1.8.0
    SEQCROW: 1.5.10
    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
    threed-strudel: 0.9.18
    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 Eric Pettersen, 3 years ago

Cc:	Greg Couch added
Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Didn't find section 'Peptide bond' in tab 'ISOLDE'

comment:2 by Tristan Croll, 3 years ago

Resolution:	→ limitation
Status:	assigned → closed

Currently you need to restart ChimeraX after installing ISOLDE for the first time, since its additions to the ChimeraX ribbon menu are only applied on app start. Should work fine in a fresh session - please let me know if it doesn't.

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