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
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 <https://rbvi.github.io/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@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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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@cgl.ucsf.edu> Sent Time:2023-02-25 06:30:54 (Saturday) To: "张一小" <yzhang@mail.sioc.ac.cn> Cc: "ChimeraX Users Help" <chimerax-users@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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
That's great! You're welcome. --Eric
On Feb 27, 2023, at 9:34 PM, 张一小 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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@cgl.ucsf.edu> Sent Time:2023-02-25 06:30:54 (Saturday) To: "张一小" <yzhang@mail.sioc.ac.cn> Cc: "ChimeraX Users Help" <chimerax-users@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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张一小