[chimerax-users] Update pdb model in cxs session

[张一小]

Hi Eric,




The script works fantastically. I'm able to update the coordinates and keep all the settings the same. Thank you so much!




Best,

Yixiao


-----Original Messages-----
From:"Eric Pettersen" <pett at cgl.ucsf.edu>
Sent Time:2023-02-25 06:30:54 (Saturday)
To: "张一小" <yzhang at mail.sioc.ac.cn>
Cc: "ChimeraX Users Help" <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Update pdb model in cxs session

Hi Yixiao,
Atomic information is stored in session files as compressed Python data structures, not in PDB format, so there is no practical way to make the swap you are envisioning by editing a session file.  Nonetheless, using Python you could copy coordinates from the model you adjusted in Coot (assuming the adjustments didn't add/delete atoms) to the model restored from the session.  I've attached a script (copycrds.py) that if you open it ChimeraX will define a command named "copycrds" that allows you to copy coordinates from one conformer to another (e.g. copycrds #1 to #2).  The script and description is also on the ChimeraX Recipes page.


--Eric


Eric Pettersen
UCSF Computer Graphics Lab




On Feb 23, 2023, at 8:09 PM, 张一小 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:



Hi,

I'm using ChimeraX to prepare figures. I saved a session containing several pdb files and maps. (The pdb files were saved in the CXS file right?) Now, I manually adjusted one of the models in Coot. Is there a way to update the old model with the new one in the session so that all the settings, such as colors, views, showing residues, hidden ribbons can be kept and applied?"




Thanks,

Yixiao

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