<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><div class=""></div><div class=""><br class=""></div><div><blockquote type="cite" class=""><div class="">On Aug 30, 2022, at 7:57 AM, Daniel Gurnon via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thanks Elaine, this is very helpful. <div class=""><br class=""></div><div class=""><div class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="">I played around with what you sent me and although it works great, I discovered two little issues with Chimera X:</div><div class=""><br class=""></div><div class="">(1) this is really minor, but I love the "soft lighting" setting and wanted to have that be the default setting in my installation. I figured I could set "lighting soft" to execute at startup, but for me, loading a new pdb always changes the lighting back to "simple". After I change it back to soft lighting it will stay that way when I bring in new pdb files without closing the original file, but if for instance I type "close all; open 2ZTA", it's back to simple lighting again. Like I said, a minor issue. But in good ol' Chimera I appreciated that I could set it up just the way I like it.</div><div class=""><br class=""></div><div class="">(2) In the color actions GUI, the radio buttons for applying color aren't being incorporated into the command. For example, if I uncheck everything except atoms/bonds, and then click "color by heteroatom", it runs "color byhetero", which applies to all.</div><div class=""><br class=""></div><div class="">I had been using 1.3, but I updated to the latest daily build and still have the same issues.</div><div class="">Dan</div></div></div></div></div></div></div><div class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><br class=""></div><div dir="ltr" class=""><span style="font-size:12.8px" class="">_</span><span style="font-size:12.8px" class="">_</span><span style="font-size:12.8px" class="">__________________________</span><br class=""></div><div dir="ltr" class=""><br class=""></div><div dir="ltr" class="">Daniel Gurnon, Ph. D.<div class="">Associate Professor of Chemistry and Biochemistry</div><div class="">DePauw University<br class=""></div><div class="">Greencastle, IN 46135</div></div></div></div></div></div></div></div></div></div><br class=""></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Aug 29, 2022 at 2:38 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class="">Hi Dan,<div class="">Thanks for using Chimera & ChimeraX in your teaching!</div><div class=""><br class=""></div><div class="">We do plan to have a Render by Attribute tool in ChimeraX, at least for the coloring part. However, it's a rather complicated GUI that we are still working on implementing from scratch (since ChimeraX uses different toolkits than Chimera).</div><div class=""><br class=""></div><div class="">ChimeraX does already have the command implementation, "color byattribute"</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute" target="_blank" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute</a>></div><div class=""><br class=""></div><div class="">Although kdHydrophobicity of amino acid residues is not automatically assigned as an attribute in ChimeraX, we provide:</div><div class=""><br class=""></div><div class="">(1) a file for loading it as an attribute, e.g. download this file as plain text and then use command "open kdHydrophobicity.defattr"</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/formats/kdHydrophobicity.defattr" target="_blank" class="">https://rbvi.ucsf.edu/chimerax/docs/user/formats/kdHydrophobicity.defattr</a>></div><div class=""><br class=""></div><div class="">...after which you could color by attribute with the command, or select residues based on their attribute values, label by attribute, etc. There are examples specifically for kdHydrophobicity here:</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html" target="_blank" class="">https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html</a>></div><div class=""><br class=""></div><div class="">For example, to use the same coloring scheme as in Chimera, command:</div><div class=""><br class=""></div><div class="">color byattribute kdHydrophobicity protein palette dodgerblue:white:orangered novalue gray</div><div class=""><br class=""></div><div class="">There are also files for other hydrophobicity scales, in case you're interested...</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html#examples" target="_blank" class="">https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html#examples</a>></div><div class=""><br class=""></div><div class="">(2) A ChimeraX command file (.cxc) that assigns the attribute as name "kdh" (could be changed to kdHydrophobicity if you prefer), shows the protein molecular surface, and colors it by those values using the same color scheme that was used in Chimera. The result looks somewhat different in ChimeraX than Chimera, however, since there are sharper boundaries in the molecular surface between the residues.</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc" target="_blank" class="">https://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc</a>></div><div class=""><br class=""></div><div class=""><span id="cid:182ef3f59bd6ac3a0a31"><Screen Shot 2022-08-29 at 11.30.05 AM.png></span><span id="cid:182ef3f59bd630ed8632"><Screen Shot 2022-08-29 at 11.30.27 AM.png></span></div><div class=""><br class=""></div><div class="">How to use the .cxc file to define a custom preset (i.e. will make an entry in the Presets menu):</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup" target="_blank" class="">https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup</a>></div><div class=""><br class=""></div><div class="">This .cxc file is just a starting point if you want to do something slightly different. You could remove the commands to hide protein atoms and show surface, you could change the coloring target to include atoms, etc.</div><div class=""><br class=""></div><div class="">I realize these are more steps in than in Chimera, however. If you are in control of the installation that all the students use, it would work well for you to make a custom preset. However, if they are all using their own installations on their own laptops, you could just tell the students to get the .cxc file (as plain text) and simply run the script by opening it in ChimeraX every time they want to do the coloring.</div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div 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=""></div><blockquote type="cite" class="">On Aug 29, 2022, at 9:20 AM, Daniel Gurnon via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hi all,<br class="">I use Chimera mostly for teaching purposes, and while Chimera X is definitely more user friendly for students, there are occasionally things I like from the legacy version that I can't find on a menu in the new program. One such feature is "Render by attribute". While the mlp command can create a lipophilicity surface, when I teach protein folding I like to have students visualize all atoms, with residues colored by kdHydrophobicity. Is there a simple way to implement this?<br class=""><br class="">Thanks<br class="">Dan<br class="">____________________________<br class=""><br class="">Daniel Gurnon, Ph. D.<br class="">Associate Professor of Chemistry and Biochemistry<br class="">DePauw University<br class="">Greencastle, IN 46135<br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" target="_blank" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></blockquote><br class=""></div></div></blockquote></div>
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