[Chimera-users] Exporting coarse-grained models of proteins

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 6 14:33:41 PDT 2015


Hello Hamish,
Those low-res surfaces can be made with the Multiscale Models tool (in Chimera menu under Tools… Higher-Order Structure) or the command “sym” with the “surfaces true” option; both of those can use symmetry information to generate the symmetry copies as low-res surfaces (optionally) from a single copy of the atomic coordinates (the asymmetric unit). 

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

the Multiscale Models dialog has a resolution option, and can also be used to generate one surface per chain for structures for which all the chains already have atomic coordinates loaded (for example, open the 4-chain structure 4HHB and use Multiscale Models on it).

You can export surfaces with File… Export Scene in main Chimera menu.  There are several format options, see:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>

An alternative way of making a low-res surface for any arbitrary (user-specified) set of atoms is to use the “molmap” command to simulate a density map from the atoms and then in the Volume Viewer dialog (which automatically appears) adjust the density isosurface level.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

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 Oct 6, 2015, at 2:33 AM, Hamish Todd <hamish.todd1 at googlemail.com> wrote:
> 
> Hello all,
> So sorry to bother you all but I've tried googling a lot of things and not found out how to create a coarse grained protein surface like this one. Creating a *surface* is easy of course, but where does that nice, intuitive, bulbous STMV protein come from? And when I get it, can I export the vertex and polygon data?
> Hamish




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