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<p>Here what you could try:</p>
<p><br>
</p>
<p><span style="text-decoration: underline;">First</span>, make sure your data are not twinned.
</p>
<p><br>
</p>
<p><span style="text-decoration: underline;">Second </span>(assuming your data are not twinned), use Self Rotation function (I like GLRF) to determine the exact number of copies in the asu. A search for k=45 should 'show' the existence and orientation of a
8-fold ncs axis. If you don't see anything at k=45, then you don't have 8 copies in the asu. Try different options (e.g. k=60 for 6-fold, k=90 for 4-fold, etc), ultimately k=180 should give you an equal number of 2-fold axes as the number of particles in the
asu.</p>
<p><br>
</p>
<p><span style="text-decoration: underline;">Third</span>, try MR with whatever 'geometric' model you have (better smaller then larger).
</p>
<p>Don't be bothered by low LLG values.If you have a solution that 'makes sense' (packing-wise)<br>
</p>
<p>compute self rotation functions with Icalc and compare them to those calculated with Iobs.</p>
<p>The two should look alike, if the solution is correct.</p>
<p><br>
</p>
<p><span style="text-decoration: underline;">Fourth</span>, assuming the above have worked, you need to go from a 'geometric' model to a
</p>
<p>'physical entity' to calculate phases. Mask you protomer and bootstrap real phases</p>
<p>by ncs-averaging density modification (e.g. resolve, dm, etc).</p>
<p><br>
</p>
<p><span style="text-decoration: underline;">Fifth</span>, calculate an averaged map, build/improve your initial model and used Pavel's new real_space_refinemnet module to refine it against the averaged density.
</p>
<p>Real space refinement <span class="st">has larger radius of convergence </span>
that classical rigid/positional refinement</p>
<p>and works much better at medium resolution (~4A).</p>
<p><br>
</p>
<p>Good luck!</p>
<p><br>
</p>
<p>Gino<br>
</p>
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<span style="font-size:11pt"></span><font style="font-size:11pt">Gino Cingolani, Ph.D.<br>
Professor<br>
Thomas Jefferson University<br>
Dept. of Biochemistry & Molecular Biology<br>
233 South 10th Street - Room 826<br>
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Tel: (215) 503 4573<br>
Website: http://www.cingolanilab.org<br>
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("You were not born to live like brutes, but to follow virtue and knowledge") <br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Roger Rowlett <rrowlett@colgate.edu><br>
<b>Sent:</b> Saturday, May 02, 2015 11:50 AM<br>
<b>To:</b> mohamed noor<br>
<b>Cc:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] Molecular replacement at low resolution</font>
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<p dir="ltr">Before giving up, search in all 8 possible P422 space groups, individually if necessary. You may have to relax or eliminate packing restraints to get solutions or partial solutions to inspect. Looking at packing of these solutions may give you
some clues about the true number of molecules in the ASU and eliminate dome space groups. Matthews calculations are not terribly reliable for N>2. Treat your 8 as a very rough estimate.</p>
<p dir="ltr">If Phaser doesn't work, try EPMR. Ultimately, you may not have sufficient data, but we just solved a difficult data set in P222 point group at 3.4 A with N=6, (Matthews predicted N=8). Looking at packing in Coot suggested a packing problem where
a tetramer straddled one of the 2 fold axes. Searching for 3 dimers worked nicely.</p>
<p dir="ltr">__________________<br>
Roger Rowlett<br>
Gordon & Dorothy Kline Professor<br>
Department of Chemistry<br>
Colgate University</p>
<div class="gmail_quote">On May 2, 2015 11:01 AM, "mohamed noor" <<a href="mailto:mohamed.noor34@gmail.com">mohamed.noor34@gmail.com</a>> wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
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<div>Dear developers<br>
<br>
</div>
I have a dataset to about 4 A in point group P 4 2 2 (Pointless suggests P 41 21 2). The protein is about 11 kDa and has an identity of about 50 % to my search model. Phaser calculated the eLLG to be about 5, and maybe not surprisingly, it failed even after
using Sculptor to prepare the model.<br>
<br>
</div>
It also says that solutions with Z-scores more than 8 were rejected for failing the packing test. Are there any suggestions on getting a solution?<br>
<br>
</div>
Solvent content calculation from Xtriage suggests about 8 copies in the asu. Would this be of any help in MR?<br>
<br>
</div>
Thanks.<br>
</div>
<br>
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