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<div style="direction: ltr;font-family: Arial;color: #000000;font-size: 10pt;">Qingfeng,<br>
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Just add "model_" to your pdb file name. For example, if your file name is test.pdb, change its name to<br>
model_test.pdb.<br>
<br>
Yogesh<br>
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<div><span style="color:rgb(34,34,34); font-size:small; background-color:rgb(255,255,255)"></span><font face="Arial" size="2"><span style="color:rgb(34,34,34); background-color:rgb(255,255,255)">Yogesh Gupta, PhD</span><br style="color:rgb(34,34,34)">
<span style="color:rgb(34,34,34); background-color:rgb(255,255,255)">Assistant Professor<br>
Dept. of Structural and Chemical Biology</span><br style="color:rgb(34,34,34)">
<span style="background-color:rgb(255,255,255); color:rgb(34,34,34)"></span><span style="background-color:rgb(255,255,255); color:rgb(34,34,34)">Mount Sinai</span><span style="background-color:rgb(255,255,255); color:rgb(34,34,34)"> School of Medicine<br>
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<div><font face="Arial" size="2"><span style="background-color:rgb(255,255,255); color:rgb(34,34,34)">1425 Madison Ave, Icahn/East Bldg. Room # 16-23B</span></font></div>
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<div><font face="Arial" size="2"><span style="color:rgb(34,34,34); background-color:rgb(255,255,255)">New York, NY 10029</span></font><font face="Arial" size="2"><span style="color:rgb(34,34,34); background-color:rgb(255,255,255)"><font size="2"><span style="color:rgb(34,34,34); background-color:rgb(255,255,255)"></span></font></span><br style="color:rgb(34,34,34)">
<span style="color:rgb(34,34,34); background-color:rgb(255,255,255)">Tel: +1-212-659-8713<br>
<a href="http://www.mountsinai.org/profiles/yogesh-gupta">http://www.mountsinai.org/profiles/yogesh-gupta</a><br style="color:rgb(34,34,34); font-size:small">
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<div style="direction: ltr;" id="divRpF588793"><font face="Tahoma" color="#000000" size="2"><b>From:</b> sharp-discuss [sharp-discuss-bounces@globalphasing.com] on behalf of Kevin [chenqf@gmail.com]<br>
<b>Sent:</b> Wednesday, April 22, 2015 7:47 PM<br>
<b>To:</b> sharp-discuss@globalphasing.com<br>
<b>Subject:</b> [sharp-discuss] Problem trying to use partial model as external phase information<br>
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<div dir="ltr">Hi all,
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<div>Recently I was able to get the density map of a protein at fairly low resolution (~3.8A) using
<span class="" id=":2th.1" tabindex="-1" style="background:yellow">SIRAS</span> in SHARP. Since it is a membrane protein and the secondary structures are mostly
<span class="" id=":2th.2" tabindex="-1" style="background:yellow">transmembrane</span> helices connected by loops, I was able to build a rough partial poly
<span class="" id=":2th.3" tabindex="-1" style="background:yellow">ala</span> model except some broken loop regions. I wanted to try the external phase information feature in SHARP and followed the manual to generate Hendrickson-Lattman coefficients, however,
I was not able to see my partial model in the drop down list in "Phase Improvement and Interpretation Panel". I can see some other
<span class="" id=":2th.5" tabindex="-1" style="background:yellow">pdb</span> files but not the one I uploaded, which was in the
<span class="" id=":2th.6" tabindex="-1" style="background:yellow">datafiles</span> directory when I manually checked it. Does the pdb file need some special headers in order to be visible in the list? </div>
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<div>Any help will be appreciated. </div>
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<div>Qingfeng</div>
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