Opened 5 years ago

Closed 5 years ago

#4484 closed defect (fixed)

side by side camera: background color wrong

Reported by: rjr27@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-140-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Another "camera sbs" bug. In camera sbs mode, I selected all of the structure ("select all") while the background was white. When the selection was applied, the background turned black for just the right-eye view.

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'ChimeraX-ISOLDE==1.1.0'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Requirement already satisfied: ChimeraX-AddH==2.1.3 in
/home/rjr27/.local/share/ChimeraX/1.1/site-packages (2.1.3)  
Requirement already satisfied: ChimeraX-Clipper==0.15.0 in
/home/rjr27/.local/share/ChimeraX/1.1/site-packages (0.15.0)  
Requirement already satisfied: ChimeraX-ISOLDE==1.1.0 in
/home/rjr27/.local/share/ChimeraX/1.1/site-packages (1.1.0)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (2.2)  
Requirement already satisfied: ChimeraX-Hbonds~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-AtomSearch~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Clipper==0.15.0 in
/home/rjr27/.local/share/ChimeraX/1.1/site-packages (0.15.0)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (2.1)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.2)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.2.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-AtomSearch~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Hbonds~=2.0->ChimeraX-
AddH==2.1.3) (1.2.3)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-ChemGroup~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Hbonds~=2.0->ChimeraX-
AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (2.2)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (2.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/usr/lib/ucsf-chimerax/lib/python3.7/site-packages (from ChimeraX-
Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.2)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.2.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-IO~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-
SaveCommand~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-IO~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-
SaveCommand~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Hbonds~=2.0->ChimeraX-
AddH==2.1.3) (1.2.3)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.2.1)  
Requirement already satisfied: ChimeraX-IO~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-
SaveCommand~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.2)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-AtomSearch~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Hbonds~=2.0->ChimeraX-
AddH==2.1.3) (1.2.3)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.2.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (1.0.4)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (1.0.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (2.2)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.2)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
AddH==2.1.3) (1.2.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Hbonds~=2.0->ChimeraX-
AddH==2.1.3) (1.2.3)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Atomic~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Clipper==0.15.0) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (1.0.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Hbonds~=2.0->ChimeraX-
AddH==2.1.3) (1.2.3)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (1.0.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-AddH==2.1.3) (1.0.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-AddH==2.1.3) (1.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.7/site-packages (from ChimeraX-Atomic~=1.0->ChimeraX-
AddH==2.1.3) (1.0)  
Lock 140491113182352 acquired on
/home/rjr27/.cache/ChimeraX/1.1/toolshed/bundle_info.cache.lock  
Lock 140491113182352 released on
/home/rjr27/.cache/ChimeraX/1.1/toolshed/bundle_info.cache.lock  
  

WARNING: You are using pip version 20.2.2; however, version 21.0.1 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
  

> open /home/rjr27/phaser/MR/JasonGuo/20191125_A1B10BR2_ML195_refine_182.pdb

Summary of feedback from opening
/home/rjr27/phaser/MR/JasonGuo/20191125_A1B10BR2_ML195_refine_182.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2021-03-19 Time 09:29:15 GMT +0000 (1616146155.93 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/Users/Jason/DLS/20191125/ALK1B10BR2L/ML195/Phenix/bFuLefOLZXOYfheV-SWS-
merged-aniso.mtz  
  
46 messages similar to the above omitted  
  
Chain information for 20191125_A1B10BR2_ML195_refine_182.pdb #1  
---  
Chain | Description  
A B C D | No description available  
E | No description available  
F G H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for 20191125_A1B10BR2_ML195_refine_182.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C 1.2/D | No description available  
1.2/E | No description available  
1.2/F 1.2/G 1.2/H | No description available  
1.2/I | No description available  
1.2/J | No description available  
1.2/K | No description available  
1.2/L | No description available  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> set bgColor white

> view #1/F:87

Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> camera sbs

> select all

8246 atoms, 8501 bonds, 16 pseudobonds, 1054 residues, 43 models selected  

> set bgColor white

> set bgColor black

> set bgColor white

> ~select all

Nothing selected  

> select all

8246 atoms, 8501 bonds, 16 pseudobonds, 1054 residues, 43 models selected  




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: Quadro RTX 5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 5820 Tower X-Series
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 16 Intel(R) Core(TM) i7-9800X CPU @ 3.80GHz
Cache Size: 16896 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        3.1G         97G        307M         24G        120G
	Swap:           15G          0B         15G

Graphics:
	65:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1eb0] (rev a1)	
	Subsystem: Dell Device [1028:129f]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (3)

comment:1 by pett, 5 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → side by side camera: background color wrong

Reported by Randy Read

comment:2 by Tom Goddard, 5 years ago

Yep, I see in side by side mode the background color is apparently only set for the left view. I will fix this today or tomorrow.

comment:3 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Background color for right view was wrong when a green selection outline was shown because the outline code set the OpenGL graphics clear color to black in order to compute the outline and did not reset it to the original color. I added code to reset to the original background color.

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