[chimerax-users] Help with surfaces

[Eoin Winston]

Hi Elaine,

Thank you so much! ChimeraX appears to be 99.999% way over my head but it
appears to be a fantastic tool! I have been getting by with Blender Atomic
Add-on, Meshlab, and some other free tools but these particular PDB files
are so huge only ChimeraX has been able to handle them.

I will certainly not use ChimeraX commercially without the appropriate
licensing! If you guys were to develop a Chimera 'Light' that handles
importing and exporting PDB files then I'm all in :)

Best regards,

Eoin

*Eoin Winston, *Head of Design



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On Tue, 2 Mar 2021 at 21:42, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Eoin,
> Great, glad that that was the solution!
>
> ChimeraX is free for academic, government, nonprofit, and personal use, so
> I believe you're all good.
>
> If it proves useful in the current project, maybe in the future you can
> consider it for commercial use :-)
> Best regards,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Mar 2, 2021, at 1:25 PM, Eoin Winston <eoin at nexucreative.com> wrote:
> >
> > 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
> >
> > Eoin Winston, Head of Design
> >
> > Phone: +353 877991603 | Email | Web | Instagram | Twitter
> > Raptech Ltd. t/a NEXU Science Communication is registered in Ireland as
> a private company limited by shares.
> > Registration No. 610585. Registered business address: 3 Mruigtuaithe,
> Ratoath, County Meath, Ireland. A85 Y883
> >
> >
> > 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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>
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