Coloring pdb surface by different colors
Hi I have a pdb with 10 TMH (single polypeptide protein, so only 1 chain in pdb). The first TMH are colored in green and the rest in yellow. Is there a way to create a surface that consists of both these colors? i.e. Surface corresponding to TMH's 1-5 is colored in green, while the surface corresponding to TMH's 6-10 in yellow? I tried the surface command option but it seems to color the entire surface in a uniform color. Any suggestions would be very helpful. Thanks Yaikhomba
Hi Yaikhomba, Definitely yes, you just need to specify the residue range in the "spec" (specifier) part of the "color" command. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> As explained in that help page, to color only the molecular surface for those residues (not atomic sticks, ribbons, etc.) you would include the "target s" option. For example, these commands would show molecular surface for 2gbp and color the parts of the surface orange for residues 50-100 and 126-135 in chain A: open 2gbp surface color /A:50-100,126-135 orange target s image of result attached. This page explains command-line specification (how to specify parts of the structure instead of the whole structure): <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.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 Nov 26, 2020, at 12:48 PM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I have a pdb with 10 TMH (single polypeptide protein, so only 1 chain in pdb). The first TMH are colored in green and the rest in yellow. Is there a way to create a surface that consists of both these colors? i.e. Surface corresponding to TMH's 1-5 is colored in green, while the surface corresponding to TMH's 6-10 in yellow?
I tried the surface command option but it seems to color the entire surface in a uniform color.
Any suggestions would be very helpful.
Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine Thanks - this works. On a similar note, I was thinking if we can use this surface (generated from the surface command using a pdb) to cave out the volume that this surface encloses within a cryo-EM map. The other complementary part as well would be helpful - the volume outside this surface (but enclosed within the cryo-EM map). I thought of the 'vop subtract' command but it requires 2 volumes and I am not sure how I can use the surface to subtract. Also, the surface generated does not seem to have a model number, so I am not sure where to start. I am not sure I want to use 'molmap' command using the pdb - it does not seem to overlap very well with the surface and depends on the resolution and the contour threshold specified. Just to recap, 1. how do we use the surface (generated from the pdb) to cut out volumes from a cryo-EM map? 2. if we have to end up using a molmap command to subtract the volume from the cryo-EM map, what resolution (and contour threshold) of the volume would you suggest to have a 'surface' equivalent (which I think is the solvent-accessible surface). Thanks Yaikhomba ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 27 November 2020 00:05 To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring pdb surface by different colors Hi Yaikhomba, Definitely yes, you just need to specify the residue range in the "spec" (specifier) part of the "color" command. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> As explained in that help page, to color only the molecular surface for those residues (not atomic sticks, ribbons, etc.) you would include the "target s" option. For example, these commands would show molecular surface for 2gbp and color the parts of the surface orange for residues 50-100 and 126-135 in chain A: open 2gbp surface color /A:50-100,126-135 orange target s image of result attached. This page explains command-line specification (how to specify parts of the structure instead of the whole structure): <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco [cid:5777477E-3CC4-4238-8FFF-43A01A79A82E@gateway.sonic.net] On Nov 26, 2020, at 12:48 PM, Y. Mutum <ym337@cam.ac.uk<mailto:ym337@cam.ac.uk>> wrote: Hi I have a pdb with 10 TMH (single polypeptide protein, so only 1 chain in pdb). The first TMH are colored in green and the rest in yellow. Is there a way to create a surface that consists of both these colors? i.e. Surface corresponding to TMH's 1-5 is colored in green, while the surface corresponding to TMH's 6-10 in yellow? I tried the surface command option but it seems to color the entire surface in a uniform color. Any suggestions would be very helpful. Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Yaikhomba, You do not need to use molmap. You can use the "volume mask" command to mask a volume with any surface, including a molecular surface. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2020, at 3:03 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi Elaine
Thanks - this works. On a similar note, I was thinking if we can use this surface (generated from the surface command using a pdb) to cave out the volume that this surface encloses within a cryo-EM map. The other complementary part as well would be helpful - the volume outside this surface (but enclosed within the cryo-EM map).
I thought of the 'vop subtract' command but it requires 2 volumes and I am not sure how I can use the surface to subtract. Also, the surface generated does not seem to have a model number, so I am not sure where to start.
I am not sure I want to use 'molmap' command using the pdb - it does not seem to overlap very well with the surface and depends on the resolution and the contour threshold specified.
Just to recap, • how do we use the surface (generated from the pdb) to cut out volumes from a cryo-EM map? • if we have to end up using a molmap command to subtract the volume from the cryo-EM map, what resolution (and contour threshold) of the volume would you suggest to have a 'surface' equivalent (which I think is the solvent-accessible surface).
Thanks Yaikhomba From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 27 November 2020 00:05 To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring pdb surface by different colors
Hi Yaikhomba, Definitely yes, you just need to specify the residue range in the "spec" (specifier) part of the "color" command. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>
As explained in that help page, to color only the molecular surface for those residues (not atomic sticks, ribbons, etc.) you would include the "target s" option. For example, these commands would show molecular surface for 2gbp and color the parts of the surface orange for residues 50-100 and 126-135 in chain A:
open 2gbp surface color /A:50-100,126-135 orange target s
image of result attached.
This page explains command-line specification (how to specify parts of the structure instead of the whole structure): <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2020-11-26 at 4.03.41 PM.png>
On Nov 26, 2020, at 12:48 PM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I have a pdb with 10 TMH (single polypeptide protein, so only 1 chain in pdb). The first TMH are colored in green and the rest in yellow. Is there a way to create a surface that consists of both these colors? i.e. Surface corresponding to TMH's 1-5 is colored in green, while the surface corresponding to TMH's 6-10 in yellow?
I tried the surface command option but it seems to color the entire surface in a uniform color.
Any suggestions would be very helpful.
Thanks Yaikhomba _______________________________________________ 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
Hi Elaine Thanks - will try this. On this note, I had a quick question on the molmap command. What is the molmap (contour threshold and resolution values) equivalent to in terms of the Surface generated from a pdb file? To paraphrase - how can we make the surface generated from 'molmap command' resemble the one generated from the 'surface command' ? I might not be very accurate here, as molmap generates a volume, but say my question refers to the surface of the volume generated. Thanks Yaikhomba Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, November 27, 2020 4:30:31 PM To: Y. Mutum <ym337@cam.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring pdb surface by different colors Hi Yaikhomba, You do not need to use molmap. You can use the "volume mask" command to mask a volume with any surface, including a molecular surface. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2020, at 3:03 AM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi Elaine
Thanks - this works. On a similar note, I was thinking if we can use this surface (generated from the surface command using a pdb) to cave out the volume that this surface encloses within a cryo-EM map. The other complementary part as well would be helpful - the volume outside this surface (but enclosed within the cryo-EM map).
I thought of the 'vop subtract' command but it requires 2 volumes and I am not sure how I can use the surface to subtract. Also, the surface generated does not seem to have a model number, so I am not sure where to start.
I am not sure I want to use 'molmap' command using the pdb - it does not seem to overlap very well with the surface and depends on the resolution and the contour threshold specified.
Just to recap, • how do we use the surface (generated from the pdb) to cut out volumes from a cryo-EM map? • if we have to end up using a molmap command to subtract the volume from the cryo-EM map, what resolution (and contour threshold) of the volume would you suggest to have a 'surface' equivalent (which I think is the solvent-accessible surface).
Thanks Yaikhomba From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 27 November 2020 00:05 To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring pdb surface by different colors
Hi Yaikhomba, Definitely yes, you just need to specify the residue range in the "spec" (specifier) part of the "color" command. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>
As explained in that help page, to color only the molecular surface for those residues (not atomic sticks, ribbons, etc.) you would include the "target s" option. For example, these commands would show molecular surface for 2gbp and color the parts of the surface orange for residues 50-100 and 126-135 in chain A:
open 2gbp surface color /A:50-100,126-135 orange target s
image of result attached.
This page explains command-line specification (how to specify parts of the structure instead of the whole structure): <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2020-11-26 at 4.03.41 PM.png>
On Nov 26, 2020, at 12:48 PM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi
I have a pdb with 10 TMH (single polypeptide protein, so only 1 chain in pdb). The first TMH are colored in green and the rest in yellow. Is there a way to create a surface that consists of both these colors? i.e. Surface corresponding to TMH's 1-5 is colored in green, while the surface corresponding to TMH's 6-10 in yellow?
I tried the surface command option but it seems to color the entire surface in a uniform color.
Any suggestions would be very helpful.
Thanks Yaikhomba _______________________________________________ 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
Hi Yaikhomba, There is no exact equivalent, as the ways in which the molecular surface and map (from molmap) contour surface are calculated are totally different. However, I have experimented with trying to get a (very approximately) similar look and position of those two kinds of surfaces in Chimera, and there is an example of molmap with those parameters as workaround #3 in the Chimera surface workarounds page: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> I do not recall the contour level used, and it might vary depending on the structure, so you probably still have to adjust the volume threshold (map contour level) to try to make the contour close to where the molecular surface lies. In summary: There isn't any reason to use molmap if the goal is to get something similar to the molecular surface.... just use the molecular surface. Another issue with molmap is that you have to be careful to only include the protein atoms, or else it may include ligand, solvent, etc. that would not be included if you had used the regular molecular surface approach. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2020, at 1:57 PM, Y. Mutum <ym337@cam.ac.uk> wrote:
Hi Elaine
Thanks - will try this. On this note, I had a quick question on the molmap command.
What is the molmap (contour threshold and resolution values) equivalent to in terms of the Surface generated from a pdb file?
To paraphrase - how can we make the surface generated from 'molmap command' resemble the one generated from the 'surface command' ?
I might not be very accurate here, as molmap generates a volume, but say my question refers to the surface of the volume generated.
Thanks Yaikhomba
participants (2)
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Elaine Meng -
Y. Mutum