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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Elaine,<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'>Thanks for your prompt reply on the previous issue. I have
managed to get the colours on the residues.<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'>Now I have another problem pertaining to the label. <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=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span
style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Is there a way to change the colour of the label such that it is
different from that of the residue..?<o:p></o:p></span></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span
style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>How can I change the information on the label such that only the
residue’s position is shown (omitting the residue’s name/type)?<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'>Thanks.<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'>Cheers,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Sumitro<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>
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<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"'> Elaine Meng
[mailto:meng@cgl.ucsf.edu] <br>
<b>Sent:</b> Wednesday, September 29, 2010 5:39 AM<br>
<b>To:</b> Sumitro Harjanto<br>
<b>Cc:</b> Chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] colour residue by value<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";
color:black'>Hi Sumitro,<o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal>It sounds like you might be thinking of computing the RGB
values from some other values yourself, then applying these
"manually" with the color command. You could do that -- it is
possible to use R,G,B or R,G,B,A (where A is opacity for a transparent
color) or a Tk code instead of a color name in practically all of the coloring
commands, as explained for the "color" command here:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal><<a
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html</a>><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal>However, if I understand your situation correctly, I
recommend instead that you create an attribute definition file (more about this
below) to assign values of your custom attribute to residues. You can
read in the file with the command "defattr" and then use the
"rangecolor" command to map colors to values. Then the
"rangecolor" command will do all the RGB interpolating for
you.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal><<a
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html</a>><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>As an example, here is using the command to show the values
of bfactor, which is already assigned when you open a PDB file:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>open 1zik<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>disp<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>rangecol bfactor min yellow max red<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>OR, you could give values of the attribute directly instead
of min/mid/max, for example<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>rangecol bfactor 20 blue 50 red 90 yellow<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Here is the description of an attribute definition file,
including links to several example files:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><<a
href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile</a>><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Then if you named your custom attribute "blah"
your commands could look something like<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>defattr /Users/me/myfiles/blah-definition.txt<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>rangecol blah min white mid 1,1,.3 max 1,.1,0<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>I hope this helps,<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Elaine<o:p></o:p></p>
</div>
<div>
<div>
<p class=MsoNormal>-----<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Elaine C. Meng, Ph.D.
<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Department of Pharmaceutical Chemistry<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>University of California, San Francisco<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<div>
<p class=MsoNormal>On Sep 28, 2010, at 2:09 AM, Sumitro Harjanto wrote:<o:p></o:p></p>
</div>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I
am looking into using CHIMERA to create a diagram. Each residue will be
coloured according to an assigned value; say if the value is high, the residue
will assume a bright red colour; if the value is low, the residue will be
coloured light yellow; residue with a medium value will appear somewhat orange.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>So
my question will be: is there a way to specify the colour of a residue by its
RGB value? And how does the command look like (as I will be scripting to do it
in large scale)?<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Thanks!
=]<o:p></o:p></span></p>
</div>
</div>
</blockquote>
</div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<DIV>
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