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Hi Elaine and Team</div>
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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.</div>
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Suppose the outer surface of the pdb-model has been colored by hydrophobicity (mlp). Then, I slice the model using the 'side view' tool. <span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">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.</span></div>
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Is there a way to color the clipped surface by a different color? If not is there a way around?</div>
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The commands I have used are:</div>
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>>> open 6g2j; hide all; </div>
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<span style="background-color:rgb(255, 255, 255);display:inline !important">>>> color #1 green; <span style="background-color:rgb(255, 255, 255);display:inline !important">color /B-G,I,Q,P,R,W,q yellow;<span> </span></span> </span></div>
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<span style="background-color:rgb(255, 255, 255);display:inline !important"><span style="background-color:rgb(255, 255, 255);display:inline !important"> Then using the side view tool, clip the surface of the model to get a slice. </span>I am trying to clip
in the plane containing Chain D and B.</span></div>
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>>> mlp #1;</div>
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>>> surface cap true;</div>
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Then, I can get a clipping plane colored by-chain. If I then type</div>
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>>>color zone #1 near #1 distance 5</div>
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Then, I can get the clipped surface to change its color but this messes up the hydrophobicity of the outer surface.</div>
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Thus, </div>
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<li><span>Is there a way to color the clipped surface separately, while not messing up with the outer surface coloring (hydrophobity in this case)?</span></li><li><span>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.</span></li></ol>
<div><span>Thanks</span></div>
<div><span>Yaikhomba</span></div>
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