Re: [Chimera-users] How to subgroup the chains of oligomer pdb
Hello, If you are asking about ChimeraX, it is better to use the address chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here, instead of the older Chimera address. I don't know if this is exactly what you want but you can give a name to any set of atoms. For example, open your-oligomer.pdb name frozen mygroup1 #1/A-F name frozen mygroup2 #1/G-L select mygroup1 color mygroup2 orange See ChimeraX "name" command (your name can be something else, like gp20 instead of mygroup1): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Or, a totally different thing you could do is split the model into two different models, for example, open your-oligomer.pdb split atoms #1/A-F atoms #1/G-L That would make your model #1 into two separate models #1.1 and #1.2 with the specified sets of atoms. See ChimeraX "split" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> You can also change names of models (what is shown in the Models list) using the "rename" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2025, at 8:14 PM, sktewary via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Friends
I would like to learn how to subgroup the chains of a oligomer pdb. suppose i have a pdb with chain A to L, in which A,B,C,D,E,F belongs to gp20 and G,H,I,J,K,L belongs to gp20. My question is how to add the descriptions to these groups chains so that when the viewer look the pdb file when he selects the gp20 all the chains to this group are selected A-F.
Please give your feedback if chimerax can do it, how to do it?
...and if you mean the grouping you see in the Chain table in the Log and in the Select→Chains menu, then the PDB file would need to have corresponding COMPND records. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 26, 2025, at 12:11 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello, If you are asking about ChimeraX, it is better to use the address chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here, instead of the older Chimera address.
I don't know if this is exactly what you want but you can give a name to any set of atoms. For example,
open your-oligomer.pdb name frozen mygroup1 #1/A-F name frozen mygroup2 #1/G-L select mygroup1 color mygroup2 orange
See ChimeraX "name" command (your name can be something else, like gp20 instead of mygroup1): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html>
Or, a totally different thing you could do is split the model into two different models, for example,
open your-oligomer.pdb split atoms #1/A-F atoms #1/G-L
That would make your model #1 into two separate models #1.1 and #1.2 with the specified sets of atoms. See ChimeraX "split" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html>
You can also change names of models (what is shown in the Models list) using the "rename" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2025, at 8:14 PM, sktewary via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Friends
I would like to learn how to subgroup the chains of a oligomer pdb. suppose i have a pdb with chain A to L, in which A,B,C,D,E,F belongs to gp20 and G,H,I,J,K,L belongs to gp20. My question is how to add the descriptions to these groups chains so that when the viewer look the pdb file when he selects the gp20 all the chains to this group are selected A-F.
Please give your feedback if chimerax can do it, how to do it?
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
participants (2)
-
Elaine Meng -
Eric Pettersen