<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ibrahim,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I'm glad it helped. I've opened a Trac ticket for your request for restricted rainbow coloring, so you'll get a notification when it gets implemented. It could be quite some time before I get to it, though if others request it also it could happen sooner.</div><div><br></div><div>--Eric</div><div><br><div><div>On Nov 9, 2009, at 8:28 PM, Ibrahim Moustafa wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div lang="EN-US" link="blue" vlink="purple" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div class="Section1"><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Hi Eric,<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> Thank you very much, as usual, I got the help I expected from chimera team.<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> Actually, the conformational change for the structure I have is dramatic and involves wide range of residues. It is really painful for the eye to follow the structural change for a certain element. Coloring the residues in few colors did the job; however, the rainbow coloring using the script you sent did a much better job.<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">It would be useful if this command can be added to the chimera!.<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> Many thanks,<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> Ibrahim<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">--------------------------------------------------------------------------------------------------------------------------<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Ibrahim M. Moustafa, Ph.D.<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Biochemistry and Molecular Biology Dept.<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">201 Althouse Lab., University Park<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Pennsylvania State University<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">PA 16802<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Tel. (814) 863-8703<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Fax (814) 865-7927<o:p></o:p></span></div></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0in; padding-bottom: 0in; padding-left: 0in; "><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span>Eric Pettersen [<a href="mailto:pett@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">mailto:pett@cgl.ucsf.edu</a>]<span class="Apple-converted-space"> </span><br><b>Sent:</b><span class="Apple-converted-space"> </span>Monday, November 09, 2009 7:29 PM<br><b>To:</b><span class="Apple-converted-space"> </span>Ibrahim Moustafa<br><b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">chimera-users@cgl.ucsf.edu</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Coloring range for residues<o:p></o:p></span></div></div></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><o:p> </o:p></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; ">Hi Ibrahim,<o:p></o:p></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>I'm not 100% sure why you want to<span class="Apple-converted-space"> </span><i>rainbow</i> the highlighted part of your structure, rather than use a single color, or color the rest of the structure dark gray, or make the rest of the structure semi-transparent, or many other possible highlighting schemes.<o:p></o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Anyway, there's no way to do it without resorting to (simple) Python. Put the following in a file that ends in ".py":<o:p></o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><o:p> </o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; ">import chimera<o:p></o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; ">residues = chimera.selection.currentResidues()<o:p></o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; ">residues.sort()<o:p></o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; ">for i, r in enumerate(residues):<o:p></o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>r.highlightNum = i+1<o:p></o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><o:p> </o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Then select the residues you want highlighted in Chimera. Run the Python script by opening it with the "open" command or with the File->Open dialog. Then run this Chimera command:<o:p></o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><o:p> </o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>rangecolor highlightNum,r min blue mid white max red sel<o:p></o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><o:p> </o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; ">--Eric<o:p></o:p></div></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><o:p> </o:p></div><div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span class="apple-converted-space"><span style="font-size: 9.5pt; font-family: Helvetica, sans-serif; color: black; "> </span></span><span style="font-size: 9.5pt; font-family: Helvetica, sans-serif; color: black; ">Eric Pettersen<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span class="apple-converted-space"><span style="font-size: 9.5pt; font-family: Helvetica, sans-serif; color: black; "> </span></span><span style="font-size: 9.5pt; font-family: Helvetica, sans-serif; color: black; ">UCSF Computer Graphics Lab<o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span class="apple-converted-space"><span style="font-size: 9.5pt; font-family: Helvetica, sans-serif; color: black; "> </span></span><span style="font-size: 9.5pt; font-family: Helvetica, sans-serif; color: black; "><a href="http://www.cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">http://www.cgl.ucsf.edu</a><o:p></o:p></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 9.5pt; font-family: Helvetica, sans-serif; color: black; "><o:p> </o:p></span></div></div></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><o:p> </o:p></div><div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; ">On Nov 9, 2009, at 11:14 AM, Ibrahim Moustafa wrote:<o:p></o:p></div></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><br><br><o:p></o:p></div><div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">Dear Chimera team,<br><br> I wonder if there is a way to color a certain range of residues using rainbow.<br>I tried to use the rainbow command with atom_spec but it applied for the whole chain.<br><br> What I want to do is to color part of the structure as a rainbow (from blue-white-red) with an increasing order of residues number.<br>I just wanted to highlight a region of conformational change so the eye can follow which part of the structure has changed dramatically.<br><br><br> Thanks in advance for your help.<br><br> Ibrahim<br><br>--<o:p></o:p></span></div><div class="MsoNormal" align="center" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; text-align: center; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><hr size="3" width="95%" align="center"></span></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">Ibrahim M. Moustafa, Ph.D.<br>Biochemistry and Molecular Biology Dept.<br>201 Althouse Lab., University Park,<br>Pennsylvania State University<br>PA 16802<br><br>Tel. (814) 863-8703<br>Fax (814) 865-7927<br><br> </span><o:p></o:p></div></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; ">_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">Chimera-users@cgl.ucsf.edu</a><br><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: blue; text-decoration: underline; ">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><o:p></o:p></div></div><div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; "><o:p> </o:p></div></div></div></div></span></blockquote></div><br></div></body></html>