Re: [Chimera-users] Rename atoms...and chains, residue numbers
On Mon, Jan 25, 2010 at 4:25 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
This is actually a little trickier than it really should be in the current builds. As of tomorrow's daily build the following will work without any issues to set the name of selected atoms to 'X1': from chimera import runCommand runCommand("setattr a name X1 sel") --or-- from chimera import selection for a in selection.currentAtoms(): a.name = "X1"
Hi-
Following up on this, I'd like to offer a feature request regarding structure editing.
Two of the most common tasks I need to do when constructing a model are: renaming the chains in the structure, and renumbering stretches of residues. I can imagine two menu items similar to "Actions->Atoms/Bonds->Delete" named "Set chain ID..." and "Renumber residues from..." that could operate on the current selection.
I suspect these menu options (or something similar, maybe under "structure editing"?) would be helpful to many folks. It could be a lot faster / easier than generating the right awk line or venturing into Emacs' PDB-mode. :-)
Would this be difficult to implement?
Thanks for considering it, -Jonathan
Thanks, Jonathan for your suggestions. In the meanwhile, however, maybe one of these PDB-editing web servers will come in handy:
http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi
http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html
Both make you choose the file before you can see the options, but can do several things, including changing chain ID and renumbering. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 28, 2010, at 1:56 PM, Jonathan Sheehan wrote:
Hi- Following up on this, I'd like to offer a feature request regarding structure editing.
Two of the most common tasks I need to do when constructing a model are: renaming the chains in the structure, and renumbering stretches of residues. I can imagine two menu items similar to "Actions->Atoms/Bonds->Delete" named "Set chain ID..." and "Renumber residues from..." that could operate on the current selection.
I suspect these menu options (or something similar, maybe under "structure editing"?) would be helpful to many folks. It could be a lot faster / easier than generating the right awk line or venturing into Emacs' PDB-mode. :-)
Would this be difficult to implement?
Thanks for considering it, -Jonathan
-- Jonathan Sheehan, Ph.D. Comput. Biol. Educ. and Outreach Vanderbilt Univ. Ctr. for Struct. Biol. 5138 MRB3, 465 21st Avenue S. Nashville, TN 37232-8755 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Jonathan,
I added renaming chains and renumbering residues to the Chimera feature requests list.
http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests
I also have needed this on many ocassions.
Tom
Hi-
Following up on this, I'd like to offer a feature request regarding structure editing.
Two of the most common tasks I need to do when constructing a model are: renaming the chains in the structure, and renumbering stretches of residues. I can imagine two menu items similar to "Actions->Atoms/Bonds->Delete" named "Set chain ID..." and "Renumber residues from..." that could operate on the current selection.
I suspect these menu options (or something similar, maybe under "structure editing"?) would be helpful to many folks. It could be a lot faster / easier than generating the right awk line or venturing into Emacs' PDB-mode. :-)
Would this be difficult to implement?
Thanks for considering it, -Jonathan
participants (3)
-
Elaine Meng -
Jonathan Sheehan -
Thomas Goddard