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<div dir="ltr">Dear Sjors and Basil,</div>
<div dir="ltr">Thank you both for your suggestions. </div>
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<div style="direction:ltr">With kind regards,</div>
<div style="direction:ltr">Jay</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Sjors Scheres - MRC LMB <scheres@mrc-lmb.cam.ac.uk><br>
<b>Sent:</b> Tuesday, January 11, 2022 4:24 AM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> Re: [3dem] Refining polished particles
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<div class="PlainText">Dear Jay,<br>
<br>
The half-sets are still separated in polishing, so iterative overfitting<br>
will be avoided. Just use the particles (data.star) from Refine3D and<br>
the postprocessing STAR file from your best refinement. The higher<br>
resolution, the better, but 4A would also do.<br>
<br>
HTH,<br>
<br>
Sjors<br>
<br>
<br>
On 1/9/22 2:29 AM, Jay Rai wrote:<br>
> Dear all,<br>
> Can we use 4 angstroms reference map during refinement of polish<br>
> particles? Also can we also do only local alignment/refinement only if<br>
> the particles before polishing yield 2.5 angstroms ( with each<br>
> unfiltered half maps are 3.5 angstroms).<br>
> Do you think it will be a model bias? <br>
> Any suggestions or thought are appreciated.<br>
><br>
> With kind regards,<br>
> Jay<br>
><br>
><br>
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<br>
-- <br>
Sjors Scheres<br>
MRC Laboratory of Molecular Biology<br>
Francis Crick Avenue, Cambridge Biomedical Campus<br>
Cambridge CB2 0QH, U.K.<br>
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