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

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

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

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

  Tom


On Sep 23, 2015, at 11:09 AM, Hsin-Yi Yeh <hyeh@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
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