- ChimeraX-users - RBVI Mailing Lists

PAE and ipTM scores
by Timothy Springer 18 Aug '26

18 Aug '26

The PAE viewer in Chimerax is wonderful. I can delete residues with low confidence pLLDT in the AF3 model (B factor <55) and the PAE viewer still works (only problem is deleting whole chains). Is there a way to delete the same residues and get revised pLLDT scores? I want them per interface in a multichain complex. - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

2 1

Regarding playing a series of volumes that are not a series
by Nour Mustafa 11 Aug '26

11 Aug '26

Dear All, I was wondering if there is a way to play a few volumes as a series when they are not in fact a series? I tried running 'vseries play' then listing the volumes individually, e.g. (vseries play #1,2,3) I tried grouping them and running vseries play again with the group's ID, but that also didn't work. Or is there a way to 'label' a group as a vseries so I can run that command, for example? I couldn't find a solution through my search. The volumes were initially a group, but I had to flip them on the z-axis and that broke the series and resulted in separate individual volumes. Sometimes I also want to compare volumes that are not a series by playing them. Thank you all in advance. Kind regards,

2 1

clip
by Timothy Springer 10 Aug '26

10 Aug '26

Can you translate this into a clip command I can use in a .cxc file? clip list Using 2 clip planes: near offset -3.0783, axis -0.462,-0.880,0.109, point on plane 218.1,184.5,202.4) far offset 12.676, axis 0.462,0.880,-0.109, point on plane 210.8,170.6,204.1) - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

4 8

Feature request: expanded CORS options for remotecontrol
by Rich Waldo 07 Aug '26

07 Aug '26

Hello! Thank you for the work you do making structural biology possible! I was wondering if it would be possible to allow the remotecontrol rest start cors parameter to accept a list of allowed origins in addition to true (which I imagine would become an alias for http?://localhost:*,http?://127.0.0.1:*) or false. I have a browser extension I've written to make downloading volumes from CryoSPARC easier and I'd like to tell ChimeraX to first try opening the destination filename and only download the volume if that fails, but since my origin is not localhost I'm blocked by CORS and can't tell whether opening the volume succeeds or fails.

2 2

Opening a PYMOL pse file
by James Prestegard 07 Aug '26

07 Aug '26

Is there a simple way to open a PYMOL pse file in chimera?

2 1

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

3 4

sequence viewer colors following a select
by Steven Brawer 06 Aug '26

06 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.

3 5

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,

2 1

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

2 1

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

1 0