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

Jakob Suckale jakob.suckale at uni-tuebingen.de
Fri Mar 4 08:00:46 PST 2016


Perfect. Thanks ever to much Elaine.

All the best,

Jakob

On 4 March 2016 at 01:54, Elaine Meng <meng at 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 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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