[3dem] Refining polished particles

[basilgreber at gmx.net]

In my experience, this should work o.k. as long as your initial angular sampling is such that the algorithm will move to finer sampling twice (or more), making sure that the refinement “settles in” properly. That said, I rarely do that, and if I do, I use slightly lower initial resolution (6 Å).

Good luck,

Basil


From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Jay Rai <jrai at fsu.edu>
Date: Sunday, 9 January 2022 at 02:31
To: 3dem <3dem-bounces at ncmir.ucsd.edu>, 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: Re: [3dem] Refining polished particles
In addition
The 4 angstroms reference map is unfiltered half maps on relion 4.

With kind regards,
Jay

________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Jay Rai <jrai at fsu.edu>
Sent: Saturday, January 8, 2022 9:29:39 PM
To: 3dem <3dem-bounces at ncmir.ucsd.edu>; 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: [3dem] Refining polished particles

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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