Cannot "color byattr" booleans

[mjc265@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.4.dev202111111002 (2021-11-11 10:02:38 UTC)
Description
(Describe the actions that caused this problem to occur here)
(Describe the actions that caused this problem to occur here)
Trying to assign attribute to specific residues. 
The defattr file opens and executes fine. The correct assignments are reported in the log. 
But when I try to color the residures with that attribute I get the error: No known/registered attribute CasEpitope. 

Where CasEpitope is the name of my attribute. 
I updated to the daily build of chimeraX but I still get the same error

Log:
UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/mjc265/Documents/COG-UK/Mono_Polyclonal Resistance/Single
> Muts Data/Structure/Raw Structural Data/Spike_P0DTC2.cif"

Spike_P0DTC2.cif title:  
Structure of SARS-CoV-2 spike at pH 5.5, all RBDs down [more info...]  
  
Chain information for Spike_P0DTC2.cif #1  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2  
  
Non-standard residues in Spike_P0DTC2.cif #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> select down

Nothing selected  

> select down

Nothing selected  

> open "C:/Users/mjc265/Documents/COG-UK/Mono_Polyclonal Resistance/Single
> Muts Data/Structure/Raw Structural Data/Spike_P0DTC2.cif" format defattr log
> true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\std_commands\defattr.py", line 105, in defattr  
name, value = line.split(": ")  
ValueError: not enough values to unpack (expected 2, got 1)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2875, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2875, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\std_commands\\__init__.py", line 81, in open  
defattr(session, data, file_name=file_name, **kw)  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\std_commands\defattr.py", line 107, in defattr  
raise SyntaxError("Line %d in %s is either not of the form 'name: value'"  
SyntaxError: Line 1 in Spike_P0DTC2.cif is either not of the form 'name:
value' or is missing initial tab  
  
SyntaxError: Line 1 in Spike_P0DTC2.cif is either not of the form 'name:
value' or is missing initial tab  
  
File "C:\Program Files\ChimeraX 1.4.dev202111111002\bin\lib\site-
packages\chimerax\std_commands\defattr.py", line 107, in defattr  
raise SyntaxError("Line %d in %s is either not of the form 'name: value'"  
  
See log for complete Python traceback.  
  

> open "C:/Users/mjc265/Documents/COG-UK/Mono_Polyclonal Resistance/Single
> Muts Data/Structure/Chimera Attributes/Cas_Epitope.defattr" format defattr
> log true

Summary of feedback from opening C:/Users/mjc265/Documents/COG-
UK/Mono_Polyclonal Resistance/Single Muts Data/Structure/Chimera
Attributes/Cas_Epitope.defattr  
---  
notes | Selector :403 matched /A ARG 403, /B ARG 403, and /C ARG 403  
Selector :417 matched /A LYS 417, /B LYS 417, and /C LYS 417  
Selector :421 matched /A TYR 421, /B TYR 421, and /C TYR 421  
Selector :453 matched /A TYR 453, /B TYR 453, and /C TYR 453  
Selector :455 matched /A LEU 455, /B LEU 455, and /C LEU 455  
Selector :456 matched /A PHE 456, /B PHE 456, and /C PHE 456  
Selector :475 matched /A ALA 475, /B ALA 475, and /C ALA 475  
Selector :476 matched /A GLY 476, /B GLY 476, and /C GLY 476  
Selector :484 matched /A GLU 484, /B GLU 484, and /C GLU 484  
Selector :485 matched /A GLY 485, /B GLY 485, and /C GLY 485  
Selector :486 matched /A PHE 486, /B PHE 486, and /C PHE 486  
Selector :487 matched /A ASN 487, /B ASN 487, and /C ASN 487  
Selector :488 matched /A CYS 488, /B CYS 488, and /C CYS 488  
Selector :489 matched /A TYR 489, /B TYR 489, and /C TYR 489  
Selector :493 matched /A GLN 493, /B GLN 493, and /C GLN 493  
Assigned attribute 'CasEpitope' to 45 residues using match mode: any  
  

> color byattribute CasEpitope :403, 417, 421, 453, 455, 456, 475, 476, 484,
> 485, 486, 487, 488, 489, 493

No known/registered attribute CasEpitope  

> save "C:/Users/mjc265/Documents/COG-UK/Mono_Polyclonal Resistance/Single
> Muts Data/Structure/working sessions/working session Cas Epitope.cxs"




OpenGL version: 3.3.0 - Build 27.20.100.8681
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude 5410
OS: Microsoft Windows 10 Enterprise (Build 18362)
Memory: 8,166,801,408
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10310U CPU @ 1.70GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
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File attachment: working session Cas Epitope.cxs

working session Cas Epitope.cxs​

[mjc265@…]

Added by email2trac

[pett]

Hi MacGregor,

That error message is misleading. I will improve it. The problem is that you cannot "color byattr" non-numeric attributes, and your CasEpitope attribute is all boolean (in fact, all True, except for residue 403 in each chain which is ' true ' so you may have to fix your .defattr file). I think you simply want to use the regular color command with an atom specifier that picks out the CasEpitope residues. For instance to color all CasEpitope residues red you could use this command:

color ::CasEpitope red

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[pett]

I have revised the error message to clarify that it needs a numeric attribute.