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 <https://www.cgl.ucsf.edu/chimerax/docs/user/formats/defattr.html> 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
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