Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring [Graphical user interface Description automatically generated] -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. [cid:image002.png@01D94092.6E8A2390] Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/
Hi Ellen It’s me again… still all the way from Belgium .. well happy new year ! I have a Chimera question for which I could not find the answer online. I want to measure the angle between 2 helices (in fact the angle between the first half and the second half of a kinked helix. I know I can define axes for each of the helices halves (giving a1 and a2), but is there a simple way to ask for computing the angles between a1 and a2 Thanks !! Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Tuesday, 14 February 2023 at 17:35 To: GOVAERTS Cédric <Cedric.Govaerts@ulb.be> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Colouring clipping plane Hi Cedric! In the Models panel, use the disclosure triangles and expand until you can see the surface cap model (see attached image) -- there will be a square color well for that model, in the column between the ID and the "eye" (show/hide). Click that color well and it should bring up your system color-editor. Then when you choose the color in that dialog it will replace the electrostatic coloring on the cap. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco [cid:61C22175-358B-40E7-A7E4-D052D4A4F04D] On Feb 14, 2023, at 7:36 AM, GOVAERTS Cédric via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:users@cgl.ucsf.edu>> wrote: Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring <image001.png> -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. <image002.png> Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/ _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Cedric! Happy new year to you too, and I hope all is well. Firstly remember that Chimera and ChimeraX are two different programs. Which one are you actually using? We use this address for ChimeraX questions and the other address chimera-users@cgl.ucsf.edu for Chimera questions. So you may want to use the latter in the future if you are really asking about Chimera. For both programs: You were almost there... if you already have axes defined, you can simply choose both rows in the Axes/Planes/Centroids dialog and the distance and angle will be reported. I.e. in ChimeraX click the row for one axis, then Cmd- (if Mac) or Ctrl-click the row for the other axis. For a command, ChimeraX is different than Chimera. In Chimera it would just be "angle a1 a2" whereas ChimeraX does not assign those IDs like a1 and a2... instead it uses the model numbers, e.g. ChimeraX commands: open 2gbp define axis perhelix true angle #1.2.5 #1.2.6 You would look in the Models list (may need to use disclosure triangle to expand to show submodels) to find out the model numbers. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2024, at 8:11 AM, GOVAERTS Cédric via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Ellen
It’s me again… still all the way from Belgium .. well happy new year !
I have a Chimera question for which I could not find the answer online. I want to measure the angle between 2 helices (in fact the angle between the first half and the second half of a kinked helix. I know I can define axes for each of the helices halves (giving a1 and a2), but is there a simple way to ask for computing the angles between a1 and a2
Thanks !!
Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/
Hi Elaine, Thanks a lot . Im' still using mostly Chimera (in fact my email was addressed to you I think). Will try. Thanks again Cedric -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, 19 January 2024 18:02 To: GOVAERTS Cédric <Cedric.Govaerts@ulb.be> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: how to measure helix-helix axis angle Hi Cedric! Happy new year to you too, and I hope all is well. Firstly remember that Chimera and ChimeraX are two different programs. Which one are you actually using? We use this address for ChimeraX questions and the other address chimera-users@cgl.ucsf.edu for Chimera questions. So you may want to use the latter in the future if you are really asking about Chimera. For both programs: You were almost there... if you already have axes defined, you can simply choose both rows in the Axes/Planes/Centroids dialog and the distance and angle will be reported. I.e. in ChimeraX click the row for one axis, then Cmd- (if Mac) or Ctrl-click the row for the other axis. For a command, ChimeraX is different than Chimera. In Chimera it would just be "angle a1 a2" whereas ChimeraX does not assign those IDs like a1 and a2... instead it uses the model numbers, e.g. ChimeraX commands: open 2gbp define axis perhelix true angle #1.2.5 #1.2.6 You would look in the Models list (may need to use disclosure triangle to expand to show submodels) to find out the model numbers. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 19, 2024, at 8:11 AM, GOVAERTS Cédric via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Ellen
It's me again. still all the way from Belgium .. well happy new year !
I have a Chimera question for which I could not find the answer online. I want to measure the angle between 2 helices (in fact the angle between the first half and the second half of a kinked helix. I know I can define axes for each of the helices halves (giving a1 and a2), but is there a simple way to ask for computing the angles between a1 and a2
Thanks !!
Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgovae rtslab.ulb.ac.be%2F&data=05%7C02%7CCedric.Govaerts%40ulb.be%7Cbe30bcdf 27984a90949b08dc1910bc27%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C 638412806890582302%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjo iV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=KWJQHtO8 wqM2t2fI6pereU1DULxhwB%2FaibhauFr0PSo%3D&reserved=0
Hi Cedric! In the Models panel, use the disclosure triangles and expand until you can see the surface cap model (see attached image) -- there will be a square color well for that model, in the column between the ID and the "eye" (show/hide). Click that color well and it should bring up your system color-editor. Then when you choose the color in that dialog it will replace the electrostatic coloring on the cap. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 14, 2023, at 7:36 AM, GOVAERTS Cédric via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX team.
I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that.
-If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring <image001.png>
-If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. <image002.png>
Can you help me getting the white clipping plane with electrostatic surface ?
Thanks a bunch
Cedric
— Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Fantastic !! Thanks — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/ From: Elaine Meng <meng@cgl.ucsf.edu> Date: Tuesday, 14 February 2023 at 17:35 To: GOVAERTS Cédric <Cedric.Govaerts@ulb.be> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Colouring clipping plane Hi Cedric! In the Models panel, use the disclosure triangles and expand until you can see the surface cap model (see attached image) -- there will be a square color well for that model, in the column between the ID and the "eye" (show/hide). Click that color well and it should bring up your system color-editor. Then when you choose the color in that dialog it will replace the electrostatic coloring on the cap. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco [cid:61C22175-358B-40E7-A7E4-D052D4A4F04D] On Feb 14, 2023, at 7:36 AM, GOVAERTS Cédric via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:users@cgl.ucsf.edu>> wrote: Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring <image001.png> -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. <image002.png> Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgovaertslab.ulb.ac.be%2F&data=05%7C01%7CCedric.Govaerts%40ulb.be%7C1ad282da5f924ac9cb1908db0ea96fb5%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638119893125316030%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JX%2BaAkY%2FUorrEndLWbfMSt7o4CUIWLeRngGhLU69iYw%3D&reserved=0> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Elaine Meng -
GOVAERTS Cédric