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#adding3dstructures


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 ?
 

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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 ?
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