[3dem] Refining polished particles

[Jay Rai]

Dear Sjors and Basil,
Thank you both for your suggestions.

With kind regards,
Jay

________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Sjors Scheres - MRC LMB <scheres at mrc-lmb.cam.ac.uk>
Sent: Tuesday, January 11, 2022 4:24 AM
To: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] Refining polished particles

Dear Jay,

The half-sets are still separated in polishing, so iterative overfitting
will be avoided. Just use the particles (data.star) from Refine3D and
the postprocessing STAR file from your best refinement. The higher
resolution, the better, but 4A would also do.

HTH,

Sjors


On 1/9/22 2:29 AM, Jay Rai wrote:
> Dear all,
> Can we use 4 angstroms reference map during refinement of polish
> particles? Also can we also do only local alignment/refinement only if
> the particles before polishing yield 2.5 angstroms ( with each
> unfiltered half maps are 3.5 angstroms).
> Do you think it will be a model bias?
> Any suggestions or thought are appreciated.
>
> With kind regards,
> Jay
>
>
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Sjors Scheres
MRC Laboratory of Molecular Biology
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