[chimerax-users] coloring clipped surface only separately

[Elaine Meng]

Hi Yaikhomba,

(1) to color the surface cap separately, just use its model number.  Use the disclosure triangles in the Model Panel to show the model numbers.  The cap is a submodel of the surface model.  You can use this model number in "color" commands or you can click its color square in the Model Panel to use the system color chooser interactively.  

See for example this screenshot with Model Panel showing that the cap model is #1.2.1, and some coloring commands for that surface in the Log:



(2) clipping plane position is saved in sessions, or within one session you can save different positions (including the position of the clipping planes) using the "view name" command, and restore them with "view" plus the name that you gave.  See
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name>

Or if you want to report clip plane position(s), see command "clip list"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html>

However, applying those numbers in a different session may not give the result you want unless you also put all the structures in the same positions as well.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 1, 2021, at 6:11 AM, Y. Mutum via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine and Team
> 
> My question relates on how we can color the 'clipped surface only' using a different color independently. This is without messing up the color of the outer surface of the model.
> 
> Suppose the outer surface of the pdb-model has been colored by hydrophobicity (mlp). Then, I slice the model using the 'side view' tool. Now, using the 'surface cap' command, I can get a clipping plane which is colored 'bychain'. However, if I try to color the clipped surface using a different color, the entire hydrophobicity surface is no longer there. These are my commands below.
> 
> Is there a way to color the clipped surface by a different color? If not is there a way around?
> The commands I have used are:
> 
> >>> open 6g2j; hide all; 
> >>> color #1 green; color /B-G,I,Q,P,R,W,q yellow;  
>     Then using the side view tool, clip the surface of the model to get a slice. I am trying to clip in the plane containing Chain D and B.
> >>> mlp #1;
> >>> surface cap true;
>     Then, I can get a clipping plane colored by-chain. If I then type
> >>>color zone #1 near #1 distance 5
>      Then, I can get the clipped surface to change its color but this messes up the hydrophobicity of the outer surface.
> 
> Thus, 
> 	• Is there a way to color the clipped surface separately, while not messing up with the outer surface coloring (hydrophobity in this case)?
> 	• Suppose I want to remember this clipping plane for another ChimeraX session and would like to avoid the manual clipping using the 'Side view'. Using command line, is there a way to get back to the clipping plane? Similar to 'camera matrix' command, but, with the 'sectioned plane' also included.
> Thanks
> Yaikhomba

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