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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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
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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