Dear ChimeraX team, When depositing models in the PDB, it is often necessary to change the nucleotide or amino acid type to “Unknown” when the resolution is not good enough to identify the register (https://www.wwpdb.org/documentation/procedure). Would it be possible to extend the functionality of the swapna and swapaa commands to support changing residues into UNK for proteins and N/DN for nucleic acids? Many thanks in advance, Matthias
Hi Matthias, So the only thing the swapaa/na commands would be doing there is changing the residue name? You can already do that with the "setattr" command. For example, to change residue 117 to DN, the command would be: setattr :117 r name DN . We will add something to the swapaa/na help pages to explicitly point this out. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Dec 19, 2023, at 1:28 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team,
When depositing models in the PDB, it is often necessary to change the nucleotide or amino acid type to “Unknown” when the resolution is not good enough to identify the register (https://www.wwpdb.org/documentation/procedure <https://www.wwpdb.org/documentation/procedure>). Would it be possible to extend the functionality of the swapna and swapaa commands to support changing residues into UNK for proteins and N/DN for nucleic acids?
Many thanks in advance,
Matthias _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
[like] Vorländer,Matthias Kopano reacted to your message: ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Tuesday, December 19, 2023 5:41:51 PM To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> Cc: ChimeraX-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Support for unknown amino acid and nucleotide Hi Matthias, So the only thing the swapaa/na commands would be doing there is changing the residue name? You can already do that with the "setattr" command. For example, to change residue 117 to DN, the command would be: setattr :117 r name DN . We will add something to the swapaa/na help pages to explicitly point this out. --Eric Eric Pettersen UCSF Computer Graphics Lab On Dec 19, 2023, at 1:28 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear ChimeraX team, When depositing models in the PDB, it is often necessary to change the nucleotide or amino acid type to “Unknown” when the resolution is not good enough to identify the register (https://www.wwpdb.org/documentation/procedure). Would it be possible to extend the functionality of the swapna and swapaa commands to support changing residues into UNK for proteins and N/DN for nucleic acids? Many thanks in advance, Matthias _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
-
Eric Pettersen -
Vorländer,Matthias Kopano