Hi, As far as I know there is no command. There is an option to "Save image" (PNG format) in the context menu of the PAE plot. To get the context menu, you have to right-click on the Plot (or on Mac, may be Ctrl-click instead). The choices in the context menu are described inthe help;: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Apr 11, 2025, at 9:35 AM, picasa1983--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I am using ChimeraX to visualize AlphaFold models and display the PAE plot with:

alphafold pae #1 /path/to/confidences.json

I would like to save only the PAE plot (not the 3D structure view) as a .png or .pdf file.

What is the correct command to save the PAE plot image in ChimeraX?

Thanks a lot!

Hi .. jalview's cli can generate pae plots on sequences for a directory of models. Docs are here: https://www.jalview.org/help/html/features/clarguments-basic.html#adding3dst... ________________________________ From: picasa1983--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 12 April 2025 10:20 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: How to save the PAE plot as an image in ChimeraX using command line ? CAUTION: This email originated from outside the University of Dundee. Do not click links or open attachments unless you recognise the sender's email address and know the content is safe. That's unfortunate, if we have 1000 simulations the only way is to do it manually ? There is no alternative package even in R or python ? _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2F&data=05%7C02%7Cj.procter%40dundee.ac.uk%7C358d1809ac6d48e9552808dd79a3a0ea%7Cae323139093a4d2a81a65d334bcd9019%7C0%7C0%7C638800465995624959%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Uh4Z2jwtKf2L1JL%2BkPFmHgtYiOZNe5vuJ6PBLDZaDZk%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/> The University of Dundee is a registered Scottish Charity, No: SC015096

Hi James, Here is some Python code that defines a savepaeplot command in ChimeraX. https://rbvi.github.io/chimerax-recipes/save_pae_plot/savepaeplot.html Tom 

On Apr 13, 2025, at 8:31 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

I'm pretty sure it could be done in ChimeraX with some python, but somebody else would have to advise on that (I don't know python).

Elaine

...

On Apr 12, 2025, at 10:51 AM, James Procter (Staff) via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi .. jalview's cli can generate pae plots on sequences for a directory of models.

Docs are here: https://www.jalview.org/help/html/features/clarguments-basic.html#adding3dst...

From: picasa1983--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 12 April 2025 10:20 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: How to save the PAE plot as an image in ChimeraX using command line ? CAUTION: This email originated from outside the University of Dundee. Do not click links or open attachments unless you recognise the sender's email address and know the content is safe.

That's unfortunate, if we have 1000 simulations the only way is to do it manually ? There is no alternative package even in R or python ? _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.u...

The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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