<div dir="ltr"><div dir="ltr"><div>Dear Pavel,</div><div><br></div><div>Thank you so much for the consideration, I have shared the file with you.</div><div><br></div><div>Best regards,</div><div>Pramod<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Oct 22, 2019 at 7:26 PM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Hi Pramod,<br>
<br>
I need to see the map and models before and after refinement to
diagnose the issue. Can you share the files? I will have a look once
I have the files.<br>
<br>
Pavel<br>
<br>
<div>On 10/22/19 10:34, pramod kumar wrote:<br>
</div>
<blockquote type="cite">
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<div>Dear Experts,</div>
<div><br>
</div>
<div>I have a map generated through cryosparc (ab
initio-reconstr and homo-refine at 3.7A* FSC and sharpened in
Scipion and separately in EMAN2). I have build the initial pdb
through BALBES which has perfect validation parameters and
nice fitting in the map (with the mtz output) but the
co-ordinates are shifted from the true origin of CS-map. I
used phenix-RSR to fit and refine, but validation results
remained too far to accept the model as good solution and also
a small region entered in wrong nearyby densities.<br>
</div>
<div><br>
</div>
<div>So far following independent and downstream approaches I
have taken:-</div>
<div><br>
</div>
<div>In phenix; dock in map, map to model, rigid body refine
followed by real space refine (with both .map and converted
.mtz), using only chain A-map boxing and model generation
through NCS.</div>
<div> <br>
</div>
<div>I have tried chimera fit for entire assembly and also only
one chain in boxed map and full map but still the validation
remained far from acceptable values and a small region in
wrong neighboring density.</div>
<div><br>
</div>
<div>Please help. <br>
</div>
<div><br>
</div>
<div><br>
-- <br>
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<div>
<div dir="ltr">
<div>
<div>Best regards,</div>
<div dir="ltr">Promod<br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
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