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