[chimerax-users] Pymol view

[Rechiche, Othman]

Hi Elaine,
Thank you for your reply.

I want to keep the matrix coordinates from a view (as from https://pymolwiki.org/index.php/Set_View) and use them in ChimeraX.
Yes views are in a PyMol session.
ChimeraX displays coordinates in a single line not as matrix.

I will look at the links you sent.

Thank you again.

Best Regards,
Othman

On Jun 23, 2022, at 6:33 PM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Of course, one can change the display styles, colors, etc. directly in ChimeraX (or Chimera).  But you are probably asking because you are more familiar with Pymol, or somebody else has given you Pymol sessions.

In case you would like to try setting up the view directly in ChimeraX, there are several example images and associated ChimeraX command scripts (.cxc files):
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Fgallery.html&data=05%7C01%7Cothman.rechiche%40psu.edu%7C20be5e2463bf40a4362908da55686c79%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637916204236478254%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Mjvp8CEJ0K%2BVzowqxIkogNb%2B5pmKbpxwagnW6IXwuYo%3D&reserved=0>
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Ffeatures.html&data=05%7C01%7Cothman.rechiche%40psu.edu%7C20be5e2463bf40a4362908da55686c79%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637916204236478254%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=88YvsbrblHnQMkQNP6Corxx%2FzhKHIR4zWzdDWWdMSMY%3D&reserved=0>

...as well as ChimeraX tutorials:
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fframetut.html&data=05%7C01%7Cothman.rechiche%40psu.edu%7C20be5e2463bf40a4362908da55686c79%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637916204236478254%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RBgGQE%2BRtFk51wZmGwQVQPF4K4GaCy76Y0nLwjPkxn8%3D&reserved=0>
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Ftutorials.html&data=05%7C01%7Cothman.rechiche%40psu.edu%7C20be5e2463bf40a4362908da55686c79%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637916204236478254%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2Bi7QZ6h2ps7YH0ah6A28lc5xIhesmbPN9eFQXgoN2DU%3D&reserved=0>

There are also many Chimera tutorials:
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Ftutorials.html&data=05%7C01%7Cothman.rechiche%40psu.edu%7C20be5e2463bf40a4362908da55686c79%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637916204236478254%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1XYoeM1SWePoDVU57yJ73ZgsFQim2GaYIGjXpSXsF2Y%3D&reserved=0>

Best,
Elaine


On Jun 23, 2022, at 1:27 PM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Othman,
Sorry no, Chimera and ChimeraX cannot read Pymol session files.  By  "view" I'm guessing you mean colors, display styles, etc.   If you meant only the orientation of the structure, maybe Pymol has an option to save a PDB file of the currently transformed coordinates, which could then be opened in Chimera or ChimeraX, but that still would not include the exact amount of zoom.

If somebody else has created a converter for Pymol session -> Chimera (or ChimeraX) session, we are not aware of it.

Best Regards,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 23, 2022, at 11:27 AM, Rechiche, Othman via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Hi everyone,
Is there a way to import/open “views” set with PyMol and open them in Chimera or ChimeraX?
Best Regards,
Othman



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220624/8955d8e4/attachment.html>