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

[Jonathan Sheehan]

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"

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