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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks this would work. I also tried the chimera workarounds to display surfaces of problematic molecules and found that changing the vdw radii
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">vdwdefine +.01<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">as suggested solved the problem. The graphics and lighting of chimeraX are nicer though.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hernando<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Tom Goddard [mailto:goddard@sonic.net]
<br>
<b>Sent:</b> Tuesday, March 06, 2018 1:01 PM<br>
<b>To:</b> chimerax-users@cgl.ucsf.edu<br>
<b>Cc:</b> Hernando J Sosa<br>
<b>Subject:</b> Re: [chimerax-users] Surfaces & color by attribute<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Hernando,<o:p></o:p></p>
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<p class="MsoNormal"> Although we don’t have the general color by attribute capability in ChimeraX yet, there is hydrophobicity surface coloring using the ChimeraX “mlp” command (molecular lipophilicity potential). For example,<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>open 1bxw<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>mlp<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Documentation<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html</a><o:p></o:p></p>
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<p class="MsoNormal">The PDB uses ChimeraX mlp for hydrophobicity images on their structure web pages, for example 1BXW image from the PDB web site below.<o:p></o:p></p>
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<p class="MsoNormal"> <a href="http://www.rcsb.org/structure/1BXW">http://www.rcsb.org/structure/1BXW</a><o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>Tom<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><img border="0" width="350" height="350" id="F4BC5AE2-5078-4257-8E14-7E2B066C718E" src="cid:image001.png@01D3B556.66CC3430"><o:p></o:p></p>
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<p class="MsoNormal">On Mar 6, 2018, at 8:12 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi Hernando,<br>
As mentioned in a recent post and also in the “Missing Features” on the download page, ChimeraX does not yet have coloring by attribute value, sorry.<br>
<br>
<<a href="http://www.rbvi.ucsf.edu/chimerax/download.html">http://www.rbvi.ucsf.edu/chimerax/download.html</a>><br>
<<a href="http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-February/000212.html">http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-February/000212.html</a>><br>
<br>
In Chimera you could try making a molmap surface, coloring the atoms under that surface by attribute, and then using Color Zone to color the surface to match the nearby atoms. See #3 in the surface workarounds page:<br>
<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
<o:p></o:p></p>
<p class="MsoNormal">On Mar 6, 2018, at 6:10 AM, Hernando J Sosa <<a href="mailto:hernando.sosa@einstein.yu.edu">hernando.sosa@einstein.yu.edu</a>> wrote:<br>
<br>
Dear ChimeraX<br>
Is it possible to color a surface by atom/residue attribute (hydrohobicity, charge)? I know it is possible to do it in ucsf-chimera but unfortunately surface calculation does not work in chimera for the files I am working on.
<br>
Thanks<br>
Hernando<o:p></o:p></p>
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