Sequence icon using probably-not-ready-for-primetime 'sequence' command

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-18.5.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-05-08)
Description
open 6cmn
show Molecule Display icons, click Sequence icon

Log:
UCSF ChimeraX version: 0.9 (2019-05-08)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6cmn format mmCIF fromDatabase pdb

Summary of feedback from opening 6cmn fetched from pdb  
---  
warning | Atom HO5' is not in the residue template for G #18 in chain D  
  
6cmn title:  
Co-Crystal Structure of HIV-1 TAR Bound to Lab-Evolved RRM TBP6.7 [more
info...]  
  
Chain information for 6cmn #1  
---  
Chain | Description  
A | TAR-Binding Protein 6.7  
D | Trans-Activation Response RNA Element  
  
  

> sequence chain selAtoms

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2631, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/cmd.py", line 127, in seqalign_chain  
raise UserError("Chains must have same sequence")  
chimerax.core.errors.UserError: Chains must have same sequence  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 89, in handle_scheme  
shortcuts.keyboard_shortcuts(self.session).run_shortcut(value)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 388, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 285, in run  
commands.run(s, f)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 38, in run  
from ..logger import user_error_format  
ImportError: cannot import name 'user_error_format' from
'chimerax.core.logger'
(/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/logger.py)  
  
ImportError: cannot import name 'user_error_format' from
'chimerax.core.logger'
(/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/logger.py)  
  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 38, in run  
from ..logger import user_error_format  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.8.38
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Eric Pettersen]

The undocumented 'sequence chain' command shows one single-sequence viewer window. Therefore, if multiple chains are given as arguments, those chains must have the same sequence (and all those chains will be associated with the sequence in the viewer window). You either need to issue a separate 'sequence chain' command for each chain, or do some preprocessing to determine the minimum number of 'sequence chain' commands you can get away with.

[Tom Goddard]

After fixing the error logging bug, the sequence icon on a multi-chain model reports: "Chains must have same sequence".

It would be nice if "sequence chain" opened a sequence panel for each separate chain. The toolbar icon can separate the chains and issue a command for each different sequence, but it seems like the wrong place to put this code.

[Eric Pettersen]

Do you mean open a separate panel regardless of whether the chains are identical or not?

[Elaine Meng]

Is it possible to use the “molecular entity” info (if available) to just show sequence for each biopolymer entity?  E.g. hemoglobin would be 2 copies of alpha chain, 2 copies of beta chain, so two sequences are shown (alpha and beta).  Maybe that’s too fancy.  If not from RCSB, would just punt to one for every single chain.

[goddard@…]

Python code could easily group all the chains with identical sequence.  Then each different sequence can be shown in its own panel.

[Eric Pettersen]

I am leaning towards adding a keyword ('coalesce') to control this behavior:

true: same behavior as now, the chains have to have the same sequence or it's an error
false: each chain shown in a separate viewer
keyword omitted: coalesce chains with identical sequence and open the minimum number of viewers possible

I currently use the 'true' behavior because the chain-summary table pre-coalesces chains and if the subsequent command doesn't agree that the sequences are the same then it should produce an error.

At any rate, the whole mess should remain undocumented/unsupported because I have no conviction that this is how I want the command to work in the long run.

[Tom Goddard]

After talking to Eric I made the sequence shortcut icon show a separate sequence panel for each unique sequence with all selected chains with that sequence associated to that panel. Also it does not log a command since the command syntax is not finalized.