Dear Chimera-users, I am new to Chimera. I saved a session.py file that manages the appearance of, say, folder1/proteinA.pdb. I would like to apply exactly the same formats, colors, etc... to proteinB.pdb located in folder2. I edited session.py but was unable to find out how to do it. It seems that the python script does not contain any line like: "open("filename","r") or anything similar. How can I reuse session.py for a new pdb file? Thanks Olivier
Hi Oliver, Sorry, there is no way simply to replace one atomic model in the session with another. (It does not simply refer to a filename.) You can open the original session, then also open the new atomic model (e.g.proteinB.pdb), and then use the command "mcopy" to copy the settings of the first model proteinA.pdb to the new one. Then you can close the first model, and then save a new session. However, the model number of proteinB.pdb in the session won't be the same as the model number of proteinA.pdb in the original session. The "mcopy" manual page includes examples: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2021, at 6:55 AM, Olivier Bignucolo <olivier.bignucolo@unil.ch> wrote:
Dear Chimera-users,
I am new to Chimera. I saved a session.py file that manages the appearance of, say, folder1/proteinA.pdb. I would like to apply exactly the same formats, colors, etc... to proteinB.pdb located in folder2.
I edited session.py but was unable to find out how to do it. It seems that the python script does not contain any line like: "open("filename","r") or anything similar.
How can I reuse session.py for a new pdb file?
Thanks Olivier
Oops, should be "Olivier" ... sorry for spelling your name wrong! Elaine
On Mar 2, 2021, at 8:19 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, Sorry, there is no way simply to replace one atomic model in the session with another. (It does not simply refer to a filename.)
You can open the original session, then also open the new atomic model (e.g.proteinB.pdb), and then use the command "mcopy" to copy the settings of the first model proteinA.pdb to the new one. Then you can close the first model, and then save a new session. However, the model number of proteinB.pdb in the session won't be the same as the model number of proteinA.pdb in the original session.
The "mcopy" manual page includes examples: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2021, at 6:55 AM, Olivier Bignucolo <olivier.bignucolo@unil.ch> wrote:
Dear Chimera-users,
I am new to Chimera. I saved a session.py file that manages the appearance of, say, folder1/proteinA.pdb. I would like to apply exactly the same formats, colors, etc... to proteinB.pdb located in folder2.
I edited session.py but was unable to find out how to do it. It seems that the python script does not contain any line like: "open("filename","r") or anything similar.
How can I reuse session.py for a new pdb file?
Thanks Olivier
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Don't worry about this! And thanks for the response. I will try it as soon as possible. Olivier ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, March 2, 2021 5:31:16 PM To: Olivier Bignucolo Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] editing session file Oops, should be "Olivier" ... sorry for spelling your name wrong! Elaine
On Mar 2, 2021, at 8:19 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, Sorry, there is no way simply to replace one atomic model in the session with another. (It does not simply refer to a filename.)
You can open the original session, then also open the new atomic model (e.g.proteinB.pdb), and then use the command "mcopy" to copy the settings of the first model proteinA.pdb to the new one. Then you can close the first model, and then save a new session. However, the model number of proteinB.pdb in the session won't be the same as the model number of proteinA.pdb in the original session.
The "mcopy" manual page includes examples: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2021, at 6:55 AM, Olivier Bignucolo <olivier.bignucolo@unil.ch> wrote:
Dear Chimera-users,
I am new to Chimera. I saved a session.py file that manages the appearance of, say, folder1/proteinA.pdb. I would like to apply exactly the same formats, colors, etc... to proteinB.pdb located in folder2.
I edited session.py but was unable to find out how to do it. It seems that the python script does not contain any line like: "open("filename","r") or anything similar.
How can I reuse session.py for a new pdb file?
Thanks Olivier
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Olivier Bignucolo