[Chimera-users] closing the surface of a monomer from a dimer PDB

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 3 16:54:59 PST 2016


Hi Jakob,
Your options are either (A) to define surface categories to enclose the sets of atom you want, or (B) to split the model into per-chain submodels.

Process (A) would be something like commands:

open 1tub
surfcat achain protein & :.a
surfcat bchain protein & :.b
surf achain
- OR - 
surf protein & :.a

surfcat manpage:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html>

Process (B) would be something like:

open 1tub
split
surf protein & #0.1
- OR -
surf protein & :.a

split manpage:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>

The ampersand stuff is to get only the protein surface.  If you just say “surf :.a” or “surf #0.1” you will also get a surface around the ligand, although it will be separately enclosed from the protein.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combinations>

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 Mar 3, 2016, at 8:08 AM, Jakob Suckale <jakob.suckale at uni-tuebingen.de> wrote:
> 
> Hi all,
> 
> I'm trying to generate a surface structure of tubulin A from a dimer
> coordinates file like 1TUB. Surfaces generated from the Action menu
> are cut open at the contact site between the monomers (see
> attachment). How can I generate a continuous surface for only one
> protein monomer?
> 
> All the best,
> 
> Jakob
> <Screen Shot 2016-03-03 at 17.00.01.jpg>_



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