[chimerax-users] Help with surfaces

[Elaine Meng]

Hi Eoin,
Not seeing the contents of your file I can't really answer very specifically, other than to say just use three molmap commands.  In each molmap command, just specify the atoms that you want to use to generate the corresponding map.  I.e. the trimer is chains A, B, C and you want to use only the protein parts of each monomer (not ligands, ions, solvent, etc.):

molmap /A & protein 20
molmap /B & protein 20
molmap /C & protein 20

Molmap command:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html>

How to specify atoms in the command line:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. I don't know if this applies to you, but ChimeraX is only free for noncommercial use.  Commercial users need to license the software as described here: https://www.rbvi.ucsf.edu/chimera/commercial_license.html

> On Mar 2, 2021, at 12:47 PM, Eoin Winston <eoin at nexucreative.com> wrote:
> 
> Hello, 
> I create molecular animations and use ChimeraX to import PDB files and convert them to surfaces which I then export for use in Autodesk 3dsmax. 
> 
> I have a very limited understanding of this fantastic software however I am wondering if there is a quick way to solve my problem.  I have a PDB file I was sent containing a trimer. When I use a command such as: 
> 
> molmap #13,1 20 (I found this on a YouTube video BTW)
> 
> It creates a surface model of the entire PDB file. How do I create separate surface models for each of the trimers? So the PDB exports with three meshes as opposed to a single mesh.
> 
> Hope that makes sense.
> Best regards,
> Eoin