Opened 4 years ago

Last modified 4 years ago

#5405 feedback defect

Problem coloring chains

Reported by: hernando.sosa@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Using the color command to color individual chains in a mutichain model appears to behave erratically.
With one  nine chains (ABCDEFGHIJKLMNOPQRS) model opened a command like:
color /K blue
does not do anything, i.e. does not color chain K blue
However if I first open a model witho nly thre chains; (ABK) and then the model with 9 chains
then it works
i .e. the command
color /K blue
colors blue chaim K of both model #1 l #2

????
 

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18.pdb

Chain information for caKIP3LAAF_M18.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
K | No description available  
  

> color /K sky blue All

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb

Summary of feedback from opening
D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb  
---  
notes | Combining 2 symmetry atoms into MG /O:802 MG  
Combining 2 symmetry atoms into MG /K:802 MG  
Combining 2 symmetry atoms into MG /N:802 MG  
Combining 2 symmetry atoms into MG /F:502 MG  
Combining 2 symmetry atoms into MG /A:502 MG  
1 messages similar to the above omitted  
  
Chain information for caKIP3LAAF_M18_3AU.pdb #2  
---  
Chain | Description  
A C E F G H | No description available  
B D I J L M | No description available  
K N O P Q R | No description available  
  

> color /K sky blue All

> close session

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18.pdb

Chain information for caKIP3LAAF_M18.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
K | No description available  
  

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb

Summary of feedback from opening
D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb  
---  
notes | Combining 2 symmetry atoms into MG /O:802 MG  
Combining 2 symmetry atoms into MG /K:802 MG  
Combining 2 symmetry atoms into MG /N:802 MG  
Combining 2 symmetry atoms into MG /F:502 MG  
Combining 2 symmetry atoms into MG /A:502 MG  
1 messages similar to the above omitted  
  
Chain information for caKIP3LAAF_M18_3AU.pdb #2  
---  
Chain | Description  
A C E F G H | No description available  
B D I J L M | No description available  
K N O P Q R | No description available  
  

> color #1 lightgreyl

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1 lightgrey

> color #2 lightgrey

> color /K cornflowerblue

> color /A orange

> select /B

6934 atoms, 7100 bonds, 862 residues, 2 models selected  

> color sel #ffaa00ff

> color sel #fea900ff

> color sel #f8a500ff

> color sel #ee9f00ff

> color sel #e89b00ff

> color sel #e29700ff

> color sel #dc9300ff

> color sel #d48d00ff

> color sel #ce8900ff

> color sel #c78500ff

> color sel #bc7d00ff

> color sel #b87b00ff

> color sel #b97b00ff

> color sel #bf7f00ff

> color sel #bf7900ff

> color sel #bf7901ff

> color sel #bf8602ff

> color sel #bf8a04ff

> color sel #bf9105ff

> color sel #bf9706ff

> color sel #bfaa09ff

> color sel #bfb009ff

> color sel #bfb00aff

> color sel #bfaa0aff

> color sel #bfa40aff

> color sel #bfa10aff

> color sel #bf9b0aff

> color sel #bf980aff

> color sel #bf920aff

> color sel #bf8c0aff

> color sel #bf890aff

> color sel #bf830aff

> color sel #bf7d0bff

> color sel #bf7a0bff

> color sel #bf7d0bff

> color sel #aaaaffff

> color /B #bf7d0b

> close session

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb

Summary of feedback from opening
D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb  
---  
notes | Combining 2 symmetry atoms into MG /O:802 MG  
Combining 2 symmetry atoms into MG /K:802 MG  
Combining 2 symmetry atoms into MG /N:802 MG  
Combining 2 symmetry atoms into MG /F:502 MG  
Combining 2 symmetry atoms into MG /A:502 MG  
1 messages similar to the above omitted  
  
Chain information for caKIP3LAAF_M18_3AU.pdb #1  
---  
Chain | Description  
A C E F G H | No description available  
B D I J L M | No description available  
K N O P Q R | No description available  
  

> color #1 lightgrey

> color /K cornflowerblue

> color /K cornflowerblue

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18.pdb

Chain information for caKIP3LAAF_M18.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
K | No description available  
  

> hide #1 models

> color /K red

> show #1 models

> close session

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb

Summary of feedback from opening
D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb  
---  
notes | Combining 2 symmetry atoms into MG /O:802 MG  
Combining 2 symmetry atoms into MG /K:802 MG  
Combining 2 symmetry atoms into MG /N:802 MG  
Combining 2 symmetry atoms into MG /F:502 MG  
Combining 2 symmetry atoms into MG /A:502 MG  
1 messages similar to the above omitted  
  
Chain information for caKIP3LAAF_M18_3AU.pdb #1  
---  
Chain | Description  
A C E F G H | No description available  
B D I J L M | No description available  
K N O P Q R | No description available  
  

> hide atoms

> show cartoons

> color /K red

> color /K red

> color /K red

> color /K red

> color /K red

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18.pdb

Chain information for caKIP3LAAF_M18.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
K | No description available  
  

> color /K red

> close session

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18.pdb

Chain information for caKIP3LAAF_M18.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
K | No description available  
  

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb

Summary of feedback from opening
D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb  
---  
notes | Combining 2 symmetry atoms into MG /O:802 MG  
Combining 2 symmetry atoms into MG /K:802 MG  
Combining 2 symmetry atoms into MG /N:802 MG  
Combining 2 symmetry atoms into MG /F:502 MG  
Combining 2 symmetry atoms into MG /A:502 MG  
1 messages similar to the above omitted  
  
Chain information for caKIP3LAAF_M18_3AU.pdb #2  
---  
Chain | Description  
A C E F G H | No description available  
B D I J L M | No description available  
K N O P Q R | No description available  
  

> color lightgray

> color /K cornflowerblue

> color /A orange

> color /B #bf7d0b

> hide #1 models

> hide #2 models

> show #1 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models




OpenGL version: 3.3.13596 Core Profile Forward-Compatible Context FireGL 18.50.02 27.20.1028.2002
OpenGL renderer: Radeon (TM) Pro WX 5100 Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: Dell Inc.
Model: Precision 5820 Tower X-Series
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 34,043,539,456
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-9820X CPU @ 3.30GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
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    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
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    ChimeraX-Movie: 1.0
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    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
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    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
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    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
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Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Depiction
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Problem coloring chains

comment:2 by Eric Pettersen, 4 years ago

Status: accepted → feedback

Hi Hernando,

I cannot reproduce this. If I open 7lup, which has 17 chains (including chain K), I can color chain K blue without any problem. Can you try 7lup and see if that structure works for you? If 7lup works for you, then it is something particular about your caKIP3LAAF_M18_3AU.pdb structure and we would need access to it to figure out the problem. You could send it to me directly (pett@…) if necessary.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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