[Chimera-users] Rendering protein molecule to a geometry format by Chimera

Tom Goddard goddard at sonic.net
Wed Sep 23 19:59:55 PDT 2015

Hi Hsin-Yi,

  There are lots of messages on the Chimera mailing list about how to identify surface exposed residues, for example,

	http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006336.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006336.html>

You can search the mailing list from the Chimera documentation web page:

	http://www.cgl.ucsf.edu/chimera/docindex.html <http://www.cgl.ucsf.edu/chimera/docindex.html>

The multiscale tool makes surfaces for each chain.  To make surfaces of any set of selected atoms use the molmap command, for example, “molmap sel 5” to make a 5 Angstrom resolution surface.  Here are molmap docs:

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

Those surfaces can be exported as OBJ with menu File / Export Scene….


> On Sep 23, 2015, at 11:09 AM, Hsin-Yi Yeh <hyeh at cse.tamu.edu> wrote:
> Hi,
> I try to render a protein molecule to a geometry format (from .pdb format to .obj format) by Chimera. I use 'Multiscale models' tool in 'Higher-Order Structure' choice and then make the model by resurfacing at some appropriate resolution. It turns out that the whole protein molecule can be modeled pretty nicely. 
> However, I now have a similar problem; instead of rendering the whole protein molecule, I would like to render the whole structure separately. I want to render the exposed residues (those residues on the surface) and non-exposed/buried residues separately, so I will have two obj files (one for the exposed residues and the others for the non-exposed residues).
> I haven't been able to figure this problem out yet. Thus, I am wondering could you please give me some direction? Any advice will be greatly appreciated!
> Thank you,
> Hsin-Yi (Cindy) Yeh
> -- 
> Hsin-Yi (Cindy) Yeh
> PhD Student
> Parasol Lab, Department of Computer Science and Engineering
> Texas A&M University
> Email: hyeh at cse.tamu.edu <mailto:hyeh at cse.tamu.edu>
> https://parasol.tamu.edu/people/hyeh/ <https://parasol.tamu.edu/people/hyeh/>_______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150923/dc5be262/attachment.html>

More information about the Chimera-users mailing list