Hi Jaewon,

You didn't attach your .defattr file, but I don't think I really need it.  The value "nan" (not a number) nonetheless is a value and therefore won't match to things looking for no/missing values.  Instead of "nan" in your defattr file, use "none".  As per the Attribute Assignment Files documentation, that will produce a Python value of None for the attribute, which is treated as a missing value.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Jul 7, 2026, at 1:09 PM, Jaewon Suk via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I am sure this question is asked often, but I could not find a solution that solved my issues even with similar contexts.

I am using a python script to prepare my .defattr files (.defattr file uploaded below). I have nan values that I would like to set as lightgray using ‘noValueColor light gray’ but to no avail. All nan values are locked in a dark gray/black color.

I saw that there was a ‘finite range’ error with numpy, that might be occurring due to my first and last values being ‘nan’, but I still have the nan coloring issue when I manually assign my first and last values as 0.0.

Other failed attempts to resolve this issue were:
- setting my noValueColor to target residues
‘target r noValueColor light gray’
- setting all ‘nan’ values to blanks
- manually rendering ’noValue’ to a specific color by Tool > StructureAnalysis > Render/ByAttribute. (The color in box is correct, but it does not render to the correct color.

Thank you!
Jaewon


_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/