Fwd: [ccpem] Help with pairing RMSD in Chimera like COOT
Dear Rajnandani and all,
I am adding in the chimerax users list (I don't know the plain chimera one) as I think this is a better question for people there.
Just to clarify, by adjust the RMSD for the map, I guess you mean scrolling the cutoff value?
Best wishes James
----- Mensaje reenviado de Alfredo Jose Florez Ariza 0000b1a72b269dbc-dmarc-request@jiscmail.ac.uk ----- Fecha: Tue, 24 Oct 2023 11:49:00 -0700 De: Alfredo Jose Florez Ariza 0000b1a72b269dbc-dmarc-request@jiscmail.ac.uk Responder-A: Alfredo Jose Florez Ariza alfredo.florez@berkeley.edu Asunto: Re: [ccpem] Help with pairing RMSD in Chimera like COOT Para: CCPEM@jiscmail.ac.uk
You mean you wanna show just the density corresponding to certain region of the model? If so, you can use volume zone command. It will be something like:
volume zone #X near #Y/Z: aaa-bbb range 3
X and Y are the ID numbers of your map and model. Z is the chain of your model and aaa and bbb are the residues you are interested in showing the map around.
The range 3 can be modified accordingly to ‘how much of your map’ you wanna show around the model region, I guess.
Alfredo
On Tue, Oct 24, 2023 at 10:24 AM Rajnandani Kashyap < rajnandani.kashyap@health.slu.edu> wrote:
Hello Everyone
I am at a stage of preparing figures for one of my manuscripts. And I was wondering if we could adjust the RMSD for the map file (density) in chimera as we do it in COOT. Basically, I want to show the electron density for a flexible N-term residues for which I do observe the density at a lower RMSD level in chimera.
Any help would be greatly appreciated.
Thanks, Rajnandani Kashyap Postdoc Fellow
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Here is my email again keeping the CCPEM list included as well as the ChimeraX one, in case people are interested in the answer.
Best wishes James
JAMES MICHAEL KRIEGER jmkrieger@cnb.csic.es escribió:
Dear Rajnandani and all,
I am adding in the chimerax users list (I don't know the plain chimera one) as I think this is a better question for people there.
Just to clarify, by adjust the RMSD for the map, I guess you mean scrolling the cutoff value?
Best wishes James
----- Mensaje reenviado de Alfredo Jose Florez Ariza 0000b1a72b269dbc-dmarc-request@jiscmail.ac.uk ----- Fecha: Tue, 24 Oct 2023 11:49:00 -0700 De: Alfredo Jose Florez Ariza 0000b1a72b269dbc-dmarc-request@jiscmail.ac.uk Responder-A: Alfredo Jose Florez Ariza alfredo.florez@berkeley.edu Asunto: Re: [ccpem] Help with pairing RMSD in Chimera like COOT Para: CCPEM@jiscmail.ac.uk
You mean you wanna show just the density corresponding to certain region of the model? If so, you can use volume zone command. It will be something like:
volume zone #X near #Y/Z: aaa-bbb range 3
X and Y are the ID numbers of your map and model. Z is the chain of your model and aaa and bbb are the residues you are interested in showing the map around.
The range 3 can be modified accordingly to ‘how much of your map’ you wanna show around the model region, I guess.
Alfredo
On Tue, Oct 24, 2023 at 10:24 AM Rajnandani Kashyap < rajnandani.kashyap@health.slu.edu> wrote:
Hello Everyone
I am at a stage of preparing figures for one of my manuscripts. And I was wondering if we could adjust the RMSD for the map file (density) in chimera as we do it in COOT. Basically, I want to show the electron density for a flexible N-term residues for which I do observe the density at a lower RMSD level in chimera.
Any help would be greatly appreciated.
Thanks, Rajnandani Kashyap Postdoc Fellow
To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
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If you just mean to change the volume contour level in ChimeraX, see "volume" command option "level" or "rmsLevel" or "sdLevel":
https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general
e.g.
volume #1 rmsLevel 1.5
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 5:36 AM, JAMES MICHAEL KRIEGER via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Here is my email again keeping the CCPEM list included as well as the ChimeraX one, in case people are interested in the answer.
Best wishes James
JAMES MICHAEL KRIEGER jmkrieger@cnb.csic.es escribió:
Dear Rajnandani and all,
I am adding in the chimerax users list (I don't know the plain chimera one) as I think this is a better question for people there.
Just to clarify, by adjust the RMSD for the map, I guess you mean scrolling the cutoff value?
Best wishes James
----- Mensaje reenviado de Alfredo Jose Florez Ariza 0000b1a72b269dbc-dmarc-request@jiscmail.ac.uk ----- Fecha: Tue, 24 Oct 2023 11:49:00 -0700 De: Alfredo Jose Florez Ariza 0000b1a72b269dbc-dmarc-request@jiscmail.ac.uk Responder-A: Alfredo Jose Florez Ariza alfredo.florez@berkeley.edu Asunto: Re: [ccpem] Help with pairing RMSD in Chimera like COOT Para: CCPEM@jiscmail.ac.uk
You mean you wanna show just the density corresponding to certain region of the model? If so, you can use volume zone command. It will be something like:
volume zone #X near #Y/Z: aaa-bbb range 3
X and Y are the ID numbers of your map and model. Z is the chain of your model and aaa and bbb are the residues you are interested in showing the map around.
The range 3 can be modified accordingly to ‘how much of your map’ you wanna show around the model region, I guess.
Alfredo
On Tue, Oct 24, 2023 at 10:24 AM Rajnandani Kashyap < rajnandani.kashyap@health.slu.edu> wrote:
Hello Everyone
I am at a stage of preparing figures for one of my manuscripts. And I was wondering if we could adjust the RMSD for the map file (density) in chimera as we do it in COOT. Basically, I want to show the electron density for a flexible N-term residues for which I do observe the density at a lower RMSD level in chimera.
Any help would be greatly appreciated.
Thanks, Rajnandani Kashyap Postdoc Fellow
To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
########################################################################
To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
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participants (2)
-
Elaine Meng -
JAMES MICHAEL KRIEGER