Hi Steffen, The answer is sort of. :-) If the file is a an mmCIF file from the PDB, then the chirality information will be present in the file. If you selected atoms of interest, then running this Python code would print the chirality information in the log: from chimerax.atomic import selected_atoms for a in selected_atoms(session): print(a, a.residue.ideal_chirality(a.name)) For convenience, I have put the above code into the attached file, which if you put the file in your home folder you could then run with "open ~/chirality.py". --Eric Eric Pettersen UCSF Computer Graphics Lab

On Jul 26, 2023, at 6:11 AM, Steffen Thomas via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I am looking for a way to determine the chirality of stereocenters. In Chimera this was possible with the command chirality. Is there such a tool possibly also for ChimeraX?

Many Thanks

Steffen

Since I see a relatively high Frequemz of contributions on the mailing list, have you thought about setting up a Discord channel or similar?

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Hi Steffen, Yes, ChimeraX’s limited capabilities in this regard would not cover your usage case. As you probably have seen, I have opened an enhancement-request ticket in our bug-tracking database for a general capability to report chirality. —Eric

On Jul 26, 2023, at 9:13 PM, Steffen Thomas via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello Eric,

many thanks for your help. But i use small molecules like sugars from ab-initio calculations (imported using SEQCROW: i will check if the ground state result has the right configuration on each carbon). And, if i understand ideal_chirality correctly, this use mmCIF informations from PDB. But such informations are not available in my case. And the scipt produces errors.

Steffen

...

Am 26.07.2023 19:43:52 schrieb Eric Pettersen <pett@cgl.ucsf.edu>:

Hi Steffen, The answer is sort of. :-) If the file is a an mmCIF file from the PDB, then the chirality information will be present in the file. If you selected atoms of interest, then running this Python code would print the chirality information in the log:

from chimerax.atomic import selected_atoms for a in selected_atoms(session): print(a, a.residue.ideal_chirality(a.name))

For convenience, I have put the above code into the attached file, which if you put the file in your home folder you could then run with "open ~/chirality.py".

--Eric

Eric Pettersen UCSF Computer Graphics Lab

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Hi Thomas, No, unfortunately no progress has occurred on chirality reporting. You would still need to resort to using Chimera to identify chirality. I'd say that implementation is still several months off, and I have added you to the recipient list for that ticket so that you will be notified when something occurs. The ticket database isn't private per se, but we avoid publicly linking to it in order to avoid having web crawlers and AI bots constantly crawling it and heavily degrading our web site's performance. --Eric Eric Pettersen UCSF Computer Graphics Lab

On Jun 19, 2025, at 11:17 PM, thomas.coudrat--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Eric,

I'm wondering about the feature discussed in this thread: the ability to identify, then label chiral centres for small molecules (information not coming from mmCIF file). This feature would be greatly useful!

I wanted to inquire about the status of this feature but I don't know how to access the bug-tracking database (maybe it's not available to the public).

Kind regards,

Thomas _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/