[Chimera-users] Rename atoms...and chains, residue numbers

Jonathan Sheehan jonathan.sheehan at gmail.com
Thu Jan 28 13:56:01 PST 2010

On Mon, Jan 25, 2010 at 4:25 PM, Eric Pettersen <pett at 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"


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 Sheehan, Ph.D.
Comput. Biol. Educ. and Outreach
Vanderbilt Univ. Ctr. for Struct. Biol.
5138 MRB3, 465 21st Avenue S.
Nashville, TN 37232-8755

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