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<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Eric,<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'> Thank you very much, as usual, I got the help I
expected from chimera team.<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'> 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></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>It would be useful if this command can be added to the chimera!.<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'> Many thanks,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> Ibrahim<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>
<div>
<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'>Ibrahim M. Moustafa, Ph.D.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Biochemistry and Molecular Biology Dept.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>201 Althouse Lab., University Park<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Pennsylvania State University<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>PA 16802<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'>Tel. (814) 863-8703<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Fax (814) 865-7927<o:p></o:p></span></p>
</div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<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"'> Eric Pettersen
[mailto:pett@cgl.ucsf.edu] <br>
<b>Sent:</b> Monday, November 09, 2009 7:29 PM<br>
<b>To:</b> Ibrahim Moustafa<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Coloring range for residues<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Ibrahim,<o:p></o:p></p>
<div>
<p class=MsoNormal><span class=apple-tab-span> </span>I'm
not 100% sure why you want to <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></p>
</div>
<div>
<p class=MsoNormal><span class=apple-tab-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></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>import chimera<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>residues = chimera.selection.currentResidues()<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>residues.sort()<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>for i, r in enumerate(residues):<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span class=apple-tab-span> </span>r.highlightNum
= i+1<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal><span class=apple-tab-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></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal><span class=apple-tab-span> </span>rangecolor
highlightNum,r min blue mid white max red sel<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>--Eric<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p style='margin:0in;margin-bottom:.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></p>
<p style='margin:0in;margin-bottom:.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></p>
<p style='margin:0in;margin-bottom:.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">http://www.cgl.ucsf.edu</a><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:9.5pt;font-family:"Helvetica","sans-serif";
color:black'><o:p> </o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p class=MsoNormal>On Nov 9, 2009, at 11:14 AM, Ibrahim Moustafa wrote:<o:p></o:p></p>
</div>
<p class=MsoNormal><br>
<br>
<o:p></o:p></p>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;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></p>
<div class=MsoNormal align=center style='text-align:center'><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
<hr size=3 width="95%" align=center>
</span></div>
<p class=MsoNormal><span style='font-size:11.0pt;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></p>
</div>
<p class=MsoNormal>_______________________________________________<br>
Chimera-users mailing list<br>
<a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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