closing the surface of a monomer from a dimer PDB
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
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>_
I should also mention that there are many possible routes to the same outcome. For example, after split or surfcat, you could still use selection and the Actions menu to show the chain A surface. If the ligand surface were also shown, you could then hide its surface with command: ~surf ligand …or with menu: Select…. Structure… ligand Actions… Surface… hide I hope this helps, Elaine
On Mar 3, 2016, at 4:54 PM, 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>_
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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>_
participants (2)
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Elaine Meng -
Jakob Suckale