<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Thomas,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Still a little sketchy on the details due to you being on the move, so I'll just describe things in general terms and maybe that'll be enough.</div><div><br></div><div>Assuming you have a StructureSequence instance (<i>i.e.</i> something returned by mol.sequences() or mol.sequence(<i>chainID</i>)), then you can use the <i>regexMatch</i> and <i>prositeMatch</i> methods I mentioned earlier to get matching indices into the sequence. Those indices are into the full sequence (<i>i.e.</i> including gaps). StructureSequence has a <b>residue</b> attribute that corresponds 1-to-1 to the <i>ungapped</i> sequence. You can map the gapped indices return by the pattern matching to ungapped indices with the sequence's <i>ungapped2gapped</i> method. One needs to be aware the the "residue" at a sequence position can be None if there is missing structure in the model.</div><div><br></div><div>Anyway, here's some example code to color a particular sequence motif red:</div><div><br></div><div># color 'ATYF' in chain A red</div><div>from chimera.colorTable import getColorByName</div><div>red = getColorByName("red")</div><div>chain = mol.sequence('A')</div><div>for match in chain.regexMatch("ATYF"):</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>u_start, u_end = [chain.gapped2ungapped(x) for x in match]</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>for res in chain.residues[u_start:u_end+1]:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>if not res:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>continue</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>res.ribbonColor = red</div><div><br></div><div>--Eric</div><div><br><div><div>On Jan 22, 2015, at 4:56 PM, Thomas Hrabe <<a href="mailto:thrabe@sanfordburnham.org">thrabe@sanfordburnham.org</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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<div>Hi Eric ,</div>
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<div>I have an algorithm that returns some subsequences of a structure and i want to color the corresponding structure segment automatically.</div>
<div>Thanks</div>
<div>Thomas<br>
<br>
from the road</div>
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Am 22.01.2015 um 16:37 schrieb Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>>:<br>
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<div>On Jan 22, 2015, at 4:21 PM, Thomas Hrabe <<a href="mailto:thrabe@sanfordburnham.org">thrabe@sanfordburnham.org</a>> wrote:</div>
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<blockquote type="cite">Hi Chimera Team,<br>
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How can I automate the Sequence View -> Edit -> Find Subsequence Tool programmatically with the Chimera shell or better within python?</blockquote>
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<div>I don't know what your context is here exactly, but if you have a Sequence object you can use its
<i>regexMatch</i> or <i>prositeMatch</i> methods to find subsequences. They return lists of (start, end) tuples. If you need more info, provide some more detail about your usage context and I can help better.</div>
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<div>--Eric</div>
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<div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px; font-size: 16px; "><div style="margin: 0px; "><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></div><div style="margin: 0px; "><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></div><div style="margin: 0px; "><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu/">http://www.cgl.ucsf.edu</a></font></div>
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