[chimerax-users] Help with surfaces

[Eoin Winston]

Hi Elaine,

That is exactly what I needed! It worked perfectly.

Thank you for your note on licensing! I am developing some COVID-19 spike
protein visualizations in collaboration with the University of Texas at
Austin - it is not a paid gig - and they are using the images I create for
educational/outreach purposes. I have only recently installed ChimeraX
after they sent me PDB files to test and I came across the software online.
If this is considered commercial use then I will uninstall it straight away
and find another way - sorry and thank you for your help!

Best regards,

Eoin

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On Tue, 2 Mar 2021 at 21:00, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
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