Re: [chimerax-users] Help with surfaces

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 *Phone:* +353 877991603 | Email | Web http://www.nexucreative.com/ | Instagram https://www.instagram.com/NEXU.creative/ | Twitter https://twitter.com/NEXU_Science 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 21:42, Elaine Meng 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

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On Mar 2, 2021, at 1:25 PM, Eoin Winston 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 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

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On Mar 2, 2021, at 12:47 PM, Eoin Winston 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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