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/

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

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/



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