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
------------------------------
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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
------------------------------
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participants (2)
-
Elaine Meng -
JAMES MICHAEL KRIEGER