Hi Eric and Elaine,
Thanks for your suggestions.
I should probably clarify that this issue only occurs when running ChimeraX in batch mode (i.e., chimerax file.cxc). When executing the commands interactively, everything works as expected and the coloring is applied correctly.
It seems the problem was that the color byattribute command was being executed before MatchMaker had fully completed. Adding a wait command between the mm and color byattribute commands solved the issue.
Thanks again for your help.
"color byattribute" not "color attribute" ... but you probably know what I meant :-)
Sorry about that,
Elaine
> On Mar 9, 2026, at 2:43 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Only other thought is:
> Make sure that your long "color attribute" command is all on one line. In what you sent, it looks like more than one line, but I couldn't tell if it was similarly split up into multiple lines inside your cxc file.
>
> Elaine
>
>> On Mar 9, 2026, at 2:34 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>
>> Hi Francisco,
>> When I try analogous operations using PDB files 1kaw and 1eyg, the coloring comes out as expected. I have attached a .cxc file with the commands I used. Maybe you could try that file and see if it works for you, and if it does then compare it to the situation you’re having difficultly with.
>> Without access to your data files, the only thing I can offer is that you should ensure that you are displaying / looking at the chains that MatchMaker used in its matching and that are associated with the alignment. Other chains will not have their colors changed.
>>
>> --Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>>
>> <test.cxc>
>>> On Mar 8, 2026, at 7:38 AM, Francisco Murphy Pérez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>>
>>> Hi
>>> Got this cxc script (basically from copy/pasting from the log)
>>>
>>> ```
>>> open a.pdb
>>> open b.pdb
>>> open a.mtz structureModel #1
>>> open b.mtz structureModel #2
>>> mm #2.2 to #1.2 bring #2.1,3 show true
>>> color byattribute r:seq_rmsd #2.2 target scab palette 0.0237942,#0fc7cf:0.258516,white:0.493237,#9e205e
>>> key cyan-white-maroon :0.024 :0.259 :0.493 showTool false
>>> select #2.2::seq_rmsd>=0.2 & ::seq_rmsd<=0.5
>>> ```
>>> Everything seems to work, except for the coloring.
>>>
>>> Am I missing something?
>>>
>>> Thanks
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