August 2026 - ChimeraX-users - RBVI Mailing Lists

cartoon style setting
by junjie han 07 Aug '26

07 Aug '26

Hi, May I ask how I can set the cartoon thick for a specific region of a structure in ChimeraX? For instance, the command "cartoon style #1/A:10-20 thick" plays an effect on the whole #1 molecule, not only affecting the specific region #1/A:10-20. Please let me know what the appropriate command is by any chance. Thanks, Junjie

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sequence viewer colors following a select
by Steven Brawer 07 Aug '26

07 Aug '26

A basic question. Example with one model. When I make a partial selection by click-drag in a sequence viewer , which turns the sequence bright green (in the sequence viewer), then ctl-click in the background of the graphics window to deselect, that bright green color in the viewer turns brown, as below. What does this mean? Why does it do this? How to restore the original coloring? When I run the command sequence chain /A, it apparently creates a new instance of the sequence viewer (deleting the old instance). This is OK with just one model. The problem with this is that if I have several models and do this, it puts the new instance at the bottom of the other sequence viewer instances, so I have to move it if I want the same physical order as in the Model pane. This becomes annoying fast. Is there a way to restore the original coloring in the sequence viewer without completely replacing the original instance of the sequence viewer with an new instance, and leaving it where it is (in the case of several models). Thank you Steve PS: I have ransacked the documentation and tried Google, but have not found an answer. This does not mean the answer is not there, only that I missed it or didn't understand it when I saw it.

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Feature Request
by Nour Mustafa 04 Aug '26

04 Aug '26

Dear All, I was wondering if it would be possible to add a feature to the 'Erase' tool that allows us to change the shape from a sphere. It would be nice if I could just 'push in' or 'pull out' at the sphere to make it into any irregular shape I want. It would make creating masks, etc. very convenient. Sorry if this is already available, I haven't been able to find something similar from my search. Kind regards,

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problem opening pdb file with the open command
by Steven Brawer 03 Aug '26

03 Aug '26

MacOS, ChimeraX 1.12 Is there a way to stop ChimeraX from looking in the ~/Downloads/ChimeraX folder when I run the open command? When it does this, the log file always says the operation is not permitted and then I have to move the ChimeraX directory to trash, which gets annoying. It appears not to look in the ChimeraX folder consistently, but only occasionally. I do not understand this. It is mentioned in the "open" help file, but I don't see the answer to my question. Thanks Steve

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Re: sequence viewer colors following a select
by Steven Brawer 03 Aug '26

03 Aug '26

I figured this out. Ctl-Click in the sequence pane, choose Settings". In settings, choose Regions, then uncheck the second item New-region-interior (if it is checked). Save, then close the window. Steve

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