<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; "><div><div>On Mar 4, 2015, at 10:14 AM, Nishant Ray Velagapudi <<a href="mailto:nishray@uw.edu">nishray@uw.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hello Mr. Petterson,<div><br></div><div>I was looking for some help with using UCSF chimera and I was wondering if I can directly email you my question. If this is not the appropriate address, my apologies, and could you point me in the appropriate direction for support?</div></div></blockquote><div><br></div>Hi Nishant,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>You should probably send questions like these to the chimera-users mailing list. That way other people can benefit from the answer, and it also allows others to answer in the cases where I'm not really the best person for the question.</div><div><br><blockquote type="cite"><div dir="ltr"><div>My issue is that I want to automate the process of creating and saving structure based sequence alignments. It has been simple to open the file and align them, but I am not sure how to save the .fasta alignment file out. Here is what I have so far:</div><div><br></div><div><div>for fn in file_names:</div><div><span class="" style="white-space:pre"> </span>replyobj.status("Processing: " + fn)</div><div><span class="" style="white-space:pre"> </span>rc("open " + fn)</div><div><span class="" style="white-space:pre"> </span><b>rc(mm #0 #1 show true)</b></div><div><span class="" style="white-space:pre"> </span>rc("close " + fn)</div></div><div><br></div><div>The bold line is the problematic one - is there any way to write out the resulting alignment file in a programmatic fashion?</div></div></blockquote><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Yes. You can locate the MultAlign Viewer (MAV) instance using the code in this previous chimera-users mail:</div><div><br></div><div><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html</a></div><div><br></div><div>That message also describes how to save the alignment to a file, in conjunction with the info in this message:</div><div><br></div><div><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010015.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010015.html</a></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>You can search the chimera-users list from this page to see if your question has been asked previously:</div><div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/docs/feedback.html">http://www.cgl.ucsf.edu/chimera/docs/feedback.html</a></div><div><br></div><div>I hope this helps.</div><div><br></div><div>--Eric</div><br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><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></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><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></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><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></p><br class="Apple-interchange-newline"></span>
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