So your command should look like interfaces select #1/A contacting #1/B bothSides true probeRadius 1.4 area Cutoff 3500 Tom

On Mar 11, 2026, at 11:39 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Rosy,

Clicking the link in the Log will open the help page for this command, which starts with showing the typical syntax with which to run the command. In this notation, square brackets denote optional keywords, but you should not write them in your command. This is explained if you click the "Usage" link just above the command syntax.

Quoting the relevant part of the "Usage" help page:

"- optional keywords and parameters are referred to as options or are enclosed in square brackets: [ ] - mutually exclusive choices are separated by a vertical bar: | - mutually exclusive choices of a required item are grouped with parentheses: ( )

These brackets, vertical bars, and parentheses in Usage lines are merely symbolic and should not be included in the typed command."

In brief: try writing your command without the brackets and it should work.

I hope this helps! Cheers,

Guillaume

On 11/03/2026 19.09, Rosaleen Calvert via ChimeraX-users wrote:

...

Hi Chimerax *interfaces select <help:user/commands/interfaces.html#select> #1/A contacting #1/B **[bothSides true][probeRadius 1.4][area Cutoff 3500]* *Expected a keyword*

What keyword is required? Have I supplied enough info?

Kind Regards Rosy Calvert

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Hello Mrinalini, When reconstructing a 3D volume from 2D projections in cryoEM image processing, there is a 50% probability of getting either chirality. It is relatively easy to visualize why if you cast shadows of your hands: you can easily make the shadow look the same with both your right and left hand as the object casting it, despite your two hands not being the same in 3D due to chirality. But natural proteins only have L-amino acids, their alpha helices are right-handed, etc. So the correct solution in your case is not to build a model into a map of the wrong chirality, because the only way it would work in terms of stereo-chemistry would be with D-amino acids. You simply need to mirror the map. In ChimeraX, assuming your map is loaded as model #1, this command will mirror it: volume flip #1 (The resulting mirrored map will only live in your ChimeraX session, so if you want to keep it, you need to save it as an MRC file.) There is also a job to mirror a map in CryoSPARC, if this is the program you are using to process your data: https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/utili... (this is the option "flip handedness" in this job). To tell chirality only from a map, in general, you need sufficient resolution to trace the backbone, and a protein containing alpha helices: then you can determine whether they are right-handed (the correct chirality) and invert the map if they are not. Some particles have chiral features that can be identified at much lower resolution (for example the super-helical turn of DNA around nucleosomes). But it is not always easy to tell depending on particle and resolution. If auto-building programs like ModelAngelo fail or produce many short disconnected fragments when applied to a good-looking map, this is often a sign of wrong chirality. I hope this helps, Guillaume ________________________________ From: Mrinalini Ramanan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Wednesday, March 18, 2026 3:23:48 PM To: chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Easier way to reverse direction of PDB file? Dear Chimerax community, I have a molecule that has a clockwise directionality for some cryoem maps, and a counter-clockwise directionality for some maps. I see this difference in directions even after fitting each map with the fit #1 in #2 command, and am now trying to build in each map. In order to create a PDB file with both directionalities, I used PyMol to do alter_state 1, obj, y = -y, rebuild, and then exported the new molecule. Is there a command in Chimera or Chimerax to do the same operations? I tried using matrix invert to no avail. Sincerely, Mrinalini VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy