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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'>Regarding point (2): changing the content of the label, other
than using the gui menu, can I do it through command line?<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'>I am dealing with quite a large number of residues for labeling.
So if I can automate the process through scripting will be good. <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'>I came across this command <i>rlabel</i> which allows me to
label the residues, but it seems to, by default, print out labels with both residue
position along the chain and 3-letter code, which I would like to omit. I read
its documentation but doesn’t seem to allow me to change the content of
the label printed out through this command.<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'>I am exploring labelopt also, but I am not too sure if it is
helpful.<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'>Please advise, 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'>sum<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'><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, October 06, 2010 12:10 AM<br>
<b>To:</b> Sumitro Harjanto<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] changing the content and colour of labels<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Sumitro,<o:p></o:p></p>
<div>
<p class=MsoNormal>1. yes, you can change the color of the labels only, using
either the "Actions... Color" menu or the color command.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>If menu, in version 1.5 (daily build), choose
"Actions... Color... all options" and in that dialog set "coloring
applies to" to "residue labels" and then do the coloring. In
earlier versions, choose "Actions... Color... residue labels" and
then use that menu again to do the coloring. Either version, you should
probably change back from "residue labels" to "all of the
above" again after coloring the labels to avoid later confusion. <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>If command, you would just put a modifier right after the
color name. Modifiers include ",l" (letter ell) for labels,
",lr" for residue labels, etc. as documented here:<o:p></o:p></p>
</div>
<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>
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<p class=MsoNormal>Example: color hot pink,lr :52<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>to color residue label only of residue 52 hot pink. No
space after the comma.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>2. yes, use menu item "Actions... Label... Residue...
custom" to set custom residue label contents. Documented here:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><<a
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/customlabel.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/customlabel.html</a>><o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Best,<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Elaine<o:p></o:p></p>
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<p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";
color:black'>----------<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";
color:black'>Elaine C. Meng, Ph.D. <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";
color:black'>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";
color:black'>Department of Pharmaceutical Chemistry<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";
color:black'>University of California, San Francisco<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";
color:black'><o:p> </o:p></span></p>
</div>
</div>
</div>
<div>
<div>
<p class=MsoNormal>On Oct 5, 2010, at 3:14 AM, Sumitro Harjanto 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";
color:#1F497D'>Hi Elaine,</span><o:p></o:p></p>
</div>
<div>
<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.</span><o:p></o:p></p>
</div>
<div>
<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.</span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> </span><o:p></o:p></p>
</div>
<div style='margin-left:.5in'>
<p class=MsoNormal style='text-indent:-.25in'><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif";color:#1F497D'>1.</span><span
style='font-size:7.0pt;color:#1F497D'> <span
class=apple-converted-space> </span></span><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..?</span><o:p></o:p></p>
</div>
<div style='margin-left:.5in'>
<p class=MsoNormal style='text-indent:-.25in'><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif";color:#1F497D'>2.</span><span
style='font-size:7.0pt;color:#1F497D'> <span
class=apple-converted-space> </span></span><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)?</span><span class=apple-style-span><span
style='font-size:11.5pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span></span><o:p></o:p></p>
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<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks.</span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Cheers,</span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Sumitro</span><o:p></o:p></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
</div>
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