<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Hernando,<div class=""><br class=""></div><div class=""> 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,</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 1bxw</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>mlp</div><div class=""><br class=""></div><div class="">Documentation</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html" class="">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html</a></div><div class=""><br class=""></div><div class="">The PDB uses ChimeraX mlp for hydrophobicity images on their structure web pages, for example 1BXW image from the PDB web site below.</div><div class=""><br class=""></div><div class=""> <a href="http://www.rcsb.org/structure/1BXW" class="">http://www.rcsb.org/structure/1BXW</a></div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><img class="center-block img-responsive mainImage" apple-inline="yes" id="F4BC5AE2-5078-4257-8E14-7E2B066C718E" src="cid:BD109785-5A57-45D3-9C59-B93A518636F7@cgl.ucsf.edu"><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 6, 2018, at 8:12 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Hernando,<br class="">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 class=""><br class=""><<a href="http://www.rbvi.ucsf.edu/chimerax/download.html" class="">http://www.rbvi.ucsf.edu/chimerax/download.html</a>><br class=""><<a href="http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-February/000212.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-February/000212.html</a>><br class=""><br class="">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 class=""><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><blockquote type="cite" class="">On Mar 6, 2018, at 6:10 AM, Hernando J Sosa <<a href="mailto:hernando.sosa@einstein.yu.edu" class="">hernando.sosa@einstein.yu.edu</a>> wrote:<br class=""><br class="">Dear ChimeraX<br class="">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 class="">Thanks<br class="">Hernando<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>