[chimerax-users] coloring clipped surface only separately

[Y. Mutum]

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,

  1.  Is there a way to color the clipped surface separately, while not messing up with the outer surface coloring (hydrophobity in this case)?
  2.  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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