<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><br><div><div>On Jun 25, 2014, at 10:04 AM, Tom Goddard</div>Hi Oliver,</div><div><br></div><div> I fixed “rainbow helix” so it uses a new rainbow for each chain — fixed in tonight’s daily build. Also I added “rainbow strand” for coloring beta strands, and “rainbow sse” for coloring both helices and strands (secondary structure elements).</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><img height="512" width="512" apple-width="yes" apple-height="yes" apple-inline="yes" id="C99815C9-D34B-475C-935D-8CF80311C006" src="cid:A41C647C-9BA9-4D02-834F-ABCC9B8FEFB5"></div><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin: 0px;"><b>From: </b>Oliver Clarke <br></div><div style="margin: 0px;"><b>Subject: </b><b>Re: [Chimera-users] Rainbow by secondary structural element?</b><br></div><div style="margin: 0px;"><b>Date: </b>June 26, 2014 at 6:37:55 AM PDT<br></div><div style="margin: 0px;"><b>To: </b>Tom Goddard <br></div><br><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Tom, I just tried out the “rainbow helix” command in the new daily build. I like it! <div><br></div><div>Only one thing, it should operate independently within each chain I think, like for rainbow at the residue level - e.g. for an ion channel like 1BL8, helices in each chain should be colored consistently, rather than having a different color for each helix in the entire molecule - see attached snaps of 1bl8 monomer and tetramer to see what I mean - I think it should color each monomer consistently.</div><div><br></div><div>Thanks again for implementing this so fast!</div><div><br></div><div>Cheers,</div><div>Oliver.</div><div><br></div><div><img height="521" width="457" apple-width="yes" apple-height="yes" apple-inline="yes" id="76E5F576-E530-46CC-8004-FC42D9004932" src="cid:B498B52D-5DBA-4295-B101-EC6C7442DBC1@cpmc.columbia.edu"><img height="542" width="300" apple-width="yes" apple-height="yes" apple-inline="yes" id="735FAF1A-58C6-4028-9C12-E9094825F6E9" src="cid:DD9A239D-32AD-425F-8DC8-80229ADC4474@cpmc.columbia.edu"></div><div><div><div>On Jun 25, 2014, at 1:04 PM, Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Oliver,<div><br></div><div> I added a “rainbow helix” command to Chimera, in tonight’s daily build. Unfortunately it doesn’t look much different then simply using rainbow when applied to a transmembrane protein. The two image below show "rainbow helix” and “rainbow” on 2rh1.</div><div><br></div><div><2rh1_helices.jpg> <2rh1_rainbow.jpg></div><div><br></div><div>They are different since the rainbow helix command does not color the turns and beta strands, and it has constant color on each helix, but those differences are hardly noticable. I also discovered that the rainbow command only applies to whole models. So it colors all helices even if you specify only the transmembrane residue range, so “rainbow helix :29-230,263-342” gives the same coloring as “rainbow helix”.</div><div><br></div><div><span class="Apple-tab-span" style="white-space: pre;"> </span>Tom</div><div><br></div><div><br><div><div>On Jun 25, 2014, at 8:01 AM, Oliver Clarke wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi all,<br><br>Currently, the rainbow function can operate at the levels of per residue, per chain or per model.<br><br>I was wondering whether it would be feasible in a future release to add an additional level, coloring per secondary structural element?<br><br>This would be particularly handy for structures of membrane proteins, where it is often desirable to color each helix/strand a different color, while not varying the color along the helix (and not coloring residues in loops etc). <br><br>Even better would be to have separate “rainbow helix” “rainbow strand” and “rainbow secstruc” commands for finer control, but this is probably not really necessary.<br><br>Cheers,<br>Oliver.<br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br><br></blockquote></div><br></div></div></blockquote></div><br></div></div></div></blockquote><div> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Oliver,<div><br></div><div> I added a “rainbow helix” command to Chimera, in tonight’s daily build. Unfortunately it doesn’t look much different then simply using rainbow when applied to a transmembrane protein. The two image below show "rainbow helix” and “rainbow” on 2rh1.</div><div><br></div><div><span><2rh1_helices.jpg></span> <span><2rh1_rainbow.jpg></span></div><div><br></div><div>They are different since the rainbow helix command does not color the turns and beta strands, and it has constant color on each helix, but those differences are hardly noticable. I also discovered that the rainbow command only applies to whole models. So it colors all helices even if you specify only the transmembrane residue range, so “rainbow helix :29-230,263-342” gives the same coloring as “rainbow helix”.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br><div><div>On Jun 25, 2014, at 8:01 AM, Oliver Clarke wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi all,<br><br>Currently, the rainbow function can operate at the levels of per residue, per chain or per model.<br><br>I was wondering whether it would be feasible in a future release to add an additional level, coloring per secondary structural element?<br><br>This would be particularly handy for structures of membrane proteins, where it is often desirable to color each helix/strand a different color, while not varying the color along the helix (and not coloring residues in loops etc). <br><br>Even better would be to have separate “rainbow helix” “rainbow strand” and “rainbow secstruc” commands for finer control, but this is probably not really necessary.<br><br>Cheers,<br>Oliver.<br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br><br></blockquote></div><br></div></div></blockquote></div><br></body></html>