showing detergent around the protein
Hi Dmitry, Not sure I understand... it is all in the same map, I'm guessing, with density from both the detergent and the molecule(s) of interest. If there are some atoms by which you can define a distance zone (e.g. a fitted atomic structure or markers that you placed by hand), then you can try using Color Zone. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorzone.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#splitbyzone> Or you could try to erase the detergent part by hand with Map Eraser (there would still be an additional copy of the full map for displaying the region that contains detergent): <https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html> Otherwise my only other idea is to run segmentation in hopes it would separate the detergent from the rest, but I don't know if that would work. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.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 Jul 18, 2022, at 1:16 PM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Do you know how to colour the map in one colour and detergent in another? I work with membrane proteins and I would like to discriminate between density and detergent.
Thank you!
Kind regards,
Hi Dmitry, I did not know that thresholding would separate them (since I'm not a cryoEM person really). Sorry for my ignorance. In that case I suppose you could just open the map twice and threshold them differently. Or make copies of the map that have the values above or below some number zeroed out (or reset to some other value of your choice), by using "volume threshold" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#threshold> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2022, at 2:15 PM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Yes, you understood correctly – I have a 3D map where I want to separate the detergent from the protein density by colour.
I thought somehow the threshold density value should be somehow involved in that – because at a certain threshold I see no detergent...
But I will try all your proposed options.
Thank you!
Kind regards, Dmitry
Sent from Mail for Windows
From: Elaine Meng Sent: Monday, July 18, 2022 10:32 PM To: Dmitry A. Semchonok Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] showing detergent around the protein
Hi Dmitry, Not sure I understand... it is all in the same map, I'm guessing, with density from both the detergent and the molecule(s) of interest. If there are some atoms by which you can define a distance zone (e.g. a fitted atomic structure or markers that you placed by hand), then you can try using Color Zone. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorzone.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#splitbyzone>
Or you could try to erase the detergent part by hand with Map Eraser (there would still be an additional copy of the full map for displaying the region that contains detergent): <https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html>
Otherwise my only other idea is to run segmentation in hopes it would separate the detergent from the rest, but I don't know if that would work. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.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 Jul 18, 2022, at 1:16 PM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Do you know how to colour the map in one colour and detergent in another? I work with membrane proteins and I would like to discriminate between density and detergent.
Thank you!
Kind regards,
Or you could just have two isosurfaces on the same map (two thresholds on the same histogram, assigned two different colors). You can add a threshold using the right-click (Ctrl-click on Mac trackpad) context menu on the Volume Viewer histogram, or use the "volume" command with multiple "level" and "color" arguments. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general> Elaine
On Jul 18, 2022, at 2:21 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dmitry, I did not know that thresholding would separate them (since I'm not a cryoEM person really). Sorry for my ignorance.
In that case I suppose you could just open the map twice and threshold them differently. Or make copies of the map that have the values above or below some number zeroed out (or reset to some other value of your choice), by using "volume threshold" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#threshold>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 18, 2022, at 2:15 PM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Yes, you understood correctly – I have a 3D map where I want to separate the detergent from the protein density by colour.
I thought somehow the threshold density value should be somehow involved in that – because at a certain threshold I see no detergent...
But I will try all your proposed options.
Thank you!
Kind regards, Dmitry
Sent from Mail for Windows
From: Elaine Meng Sent: Monday, July 18, 2022 10:32 PM To: Dmitry A. Semchonok Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] showing detergent around the protein
Hi Dmitry, Not sure I understand... it is all in the same map, I'm guessing, with density from both the detergent and the molecule(s) of interest. If there are some atoms by which you can define a distance zone (e.g. a fitted atomic structure or markers that you placed by hand), then you can try using Color Zone. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/colorzone.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#splitbyzone>
Or you could try to erase the detergent part by hand with Map Eraser (there would still be an additional copy of the full map for displaying the region that contains detergent): <https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html>
Otherwise my only other idea is to run segmentation in hopes it would separate the detergent from the rest, but I don't know if that would work. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.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 Jul 18, 2022, at 1:16 PM, Dmitry A. Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Do you know how to colour the map in one colour and detergent in another? I work with membrane proteins and I would like to discriminate between density and detergent.
Thank you!
Kind regards,
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participants (2)
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Dmitry A. Semchonok -
Elaine Meng