color byattr: min() arg is an empty sequence

[guillaume.gaullier@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
I opened output files (attached) from a ConSurf job in a fresh ChimeraX session. The first sequence in the alignment got automatically associated to the structure. I then ran the command:

color byattr seq_conservation

And got the error message that prompted this bug report.

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 /Users/guillaume/Labo/DeindlLab/sequence-structure-
> analyses/ALC1-autoinhibited-7EPU/macro-
> consurf/macro_for_consurf_pdb_ATOMS_section_With_ConSurf.pdb

Summary of feedback from opening /Users/guillaume/Labo/DeindlLab/sequence-
structure-analyses/ALC1-autoinhibited-7EPU/macro-
consurf/macro_for_consurf_pdb_ATOMS_section_With_ConSurf.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 671
THR A 675 1 5  
Start residue of secondary structure not found: HELIX 2 2 PRO A 686 GLY A 688
1 3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 750 LYS A 754
1 5  
Start residue of secondary structure not found: HELIX 4 4 GLU A 802 GLU A 806
1 5  
Start residue of secondary structure not found: HELIX 5 5 GLN B 32 TRP B 39 1
8  
61 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (603 )  
Cannot find LINK/SSBOND residue CYS (746 )  
Cannot find LINK/SSBOND residue ILE (44 )  
Cannot find LINK/SSBOND residue LYS (77 )  
Cannot find LINK/SSBOND residue MG (1202 )  
1 messages similar to the above omitted  
  
Chain information for macro_for_consurf_pdb_ATOMS_section_With_ConSurf.pdb #1  
---  
Chain | Description  
B | No description available  
  

> open /Users/guillaume/Labo/DeindlLab/sequence-structure-
> analyses/ALC1-autoinhibited-7EPU/macro-consurf/query_msa_clustalw.aln

Summary of feedback from opening /Users/guillaume/Labo/DeindlLab/sequence-
structure-analyses/ALC1-autoinhibited-7EPU/macro-
consurf/query_msa_clustalw.aln  
---  
notes | Alignment identifier is query_msa_clustalw.aln  
Associated macro_for_consurf_pdb_ATOMS_section_With_ConSurf.pdb chain B to
Input_pdb_SEQRES_B with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment query_msa_clustalw.aln  
  
Opened 150 sequences from query_msa_clustalw.aln  

> color byattribute seq_conservation

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1142, in color_by_attr  
non_none_colors = _value_colors(palette, range, non_none_attr_vals)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1263, in _value_colors  
min_val, max_val = min(values), max(values)  
ValueError: min() arg is an empty sequence  
  
ValueError: min() arg is an empty sequence  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1263, in _value_colors  
min_val, max_val = min(values), max(values)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.17
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.Hardware:

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      Model Identifier: MacBookPro12,1
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      Hyper-Threading Technology: Enabled
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Software:

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      Revision ID: 0x0009
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File attachment: macro_for_consurf_pdb_ATOMS_section_With_ConSurf.pdb

macro_for_consurf_pdb_ATOMS_section_With_ConSurf.pdb​

[guillaume.gaullier@…]

Added by email2trac

[pett]

Hi Guillaume,

I suspect that this problem is now fixed, but I would need your query_msa_clustalw.aln file to test. Could you send that?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[guillaume.gaullier@…]

Hi Eric,

I wanted to attach both files but the bug report dialog would only take one. Here is the alignment file.
Cheers,

Guillaume


On 20 Jul 2021, at 18:44, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#4921: color byattr: min() arg is an empty sequence
-------------------------------------------+----------------------------
         Reporter:  guillaume.gaullier@…  |      Owner:  Eric Pettersen
             Type:  defect                |     Status:  feedback
         Priority:  normal                |  Milestone:
        Component:  Structure Analysis    |    Version:
       Resolution:                        |   Keywords:
       Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
          Project:  ChimeraX              |
-------------------------------------------+----------------------------
Changes (by Eric Pettersen):

* status:  accepted => feedback


Comment:

Hi Guillaume,
        I suspect that this problem is now fixed, but I would need your
query_msa_clustalw.aln file to test.  Could you send that?

--Eric

        Eric Pettersen
        UCSF Computer Graphics Lab

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4921#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker









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query_msa_clustalw.aln​

[guillaume.gaullier@…]

Added by email2trac

[pett]

Hi Guillaume,

Thanks for supplying the alignment. This problem is fixed in the daily build. Nonetheless, there's another, non-bug, problem: in the part of the alignment where your structure associates, over 85% of the sequences are just gaps. Therefore no sequence conservation score is computed because the "gap threshold" is 0.5 (50%). You need to right-click on the alignment and choose "Settings..." from the context menu. In the Headers tab of the Settings dialog go to the Conservation section and scroll down to "Gap fraction" and increase it to 0.9. This will get conservation scores computed for the residues of your structure and you can then use "color byattr..." Actually, doing this will also get things to work in the build you currently have as well.

--Eric

[guillaume.gaullier@…]

Thank you! Now that you mention it, I think this is mainly because I requested Consurf to give me 150 sequences that uniformly sample all homologues returned by the search, but I can also request the 150 sequences that align best to the query and that should fix the problem too since I would expect the best aligning sequences to have less gaps (or if they don’t, I’ll have learned that this particular domain is surprisingly divergent from the rest of all macro domains).

Good to know that everything works as it should in ChimeraX. I was perplexed by this error, I normally run into errors of the kind that tell me in the Log how I messed up my command.

Thank you again, and sorry I added some noise to the bug tracker.

Guillaume


On 20 Jul 2021, at 21:04, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#4921: color byattr: min() arg is an empty sequence
-------------------------------------------+----------------------------
         Reporter:  guillaume.gaullier@…  |      Owner:  Eric Pettersen
             Type:  defect                |     Status:  closed
         Priority:  normal                |  Milestone:
        Component:  Structure Analysis    |    Version:
       Resolution:  fixed                 |   Keywords:
       Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
          Project:  ChimeraX              |
-------------------------------------------+----------------------------
Changes (by Eric Pettersen):

* status:  feedback => closed
* resolution:   => fixed


Comment:

Hi Guillaume,
        Thanks for supplying the alignment.  This problem is fixed in the
daily build.  Nonetheless, there's another, non-bug, problem: in the part
of the alignment where your structure associates, over 85% of the
sequences are just gaps.  Therefore no sequence conservation score is
computed because the "gap threshold" is 0.5 (50%).  You need to right-
click on the alignment and choose "Settings..." from the context menu.  In
the Headers tab of the Settings dialog go to the Conservation section and
scroll down to "Gap fraction" and increase it to 0.9.  This will get
conservation scores computed for the residues of your structure and you
can then use "color byattr..."  Actually, doing this will also get things
to work in the build you currently have as well.

--Eric

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4921#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker









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E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

[pett]

No, thanks for reporting the problem. It is a bug in the production release that has subsequently been fixed in the daily build, but it was a bug!