change chain description

Hello, When I load a pdb into chimerax, a table appears with the chain IDs and associated descriptions. I would like to change the chain descriptions. How do I do that? Thank you, J

Hi Joshua, ChimeraX gets the chain descriptions from a PDB file by processing the COMPND records, specifically the MOL_ID, MOLECULE, CHAIN, and SYNONYM "sub-records" of the COMPND records, as per the somewhat ugly code at lines 1482-1525 of atomic/src/structure.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/structu...>. For mmCIF files, it does analogous things by processing the struct_asym and entity tables. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Mar 26, 2024, at 12:04 PM, Joshua Arribere via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
When I load a pdb into chimerax, a table appears with the chain IDs and associated descriptions. I would like to change the chain descriptions. How do I do that?
Thank you,
J _______________________________________________ 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/

Hi, I don't know how to do it from ChimeraX, but if you open the cif or pdb file in a text editor and compare with a file from the PDB, you could figure out where and how this info is written and then write it manually in your file. If this is a file you are going to deposit to the PDB, the deposition process will collect all the necessary info from the form and generate a cif file with it, so in the end the cif file after deposition and release will contain all the info that your pre-deposition file did not have. I hope this helps, Guillaume ________________________________ From: Joshua Arribere via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Tuesday, March 26, 2024 8:04:23 PM To: chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] change chain description Hello, When I load a pdb into chimerax, a table appears with the chain IDs and associated descriptions. I would like to change the chain descriptions. How do I do that? Thank you, J 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
participants (3)
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Eric Pettersen
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Guillaume Gaullier
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Joshua Arribere