Perfect. Thanks ever to much Elaine. All the best, Jakob On 4 March 2016 at 01:54, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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@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>_