[3dem] question in post-processing

[Mohamed A Sayed]

?Hi Basil

I am attaching the outcome from the ctf refinement. Thank you very much for your help.

Best regards

________________________________
From: Basil Greber <basilgreber at gmx.net>
Sent: Sunday, May 3, 2020 6:50 PM
To: Mohamed A Sayed
Cc: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] question in post-processing

Hi Mohamed,

Have you done CTF refinement, beam tilt in particular?

Basil



Am 03.05.2020 um 07:37 schrieb Mohamed A Sayed <mohamed.sobhy at kaust.edu.sa<mailto:mohamed.sobhy at kaust.edu.sa>>:

Hello,

I hope all is safe. If you would please advise on the following:

I made auto-refinement for a structure using auto-sampling settings: Initial angular sampling 3.7, local searching from auto-sampling 1.8. The output after convergence was "Final resolution (without masking) is: 3.26154)". When I generate a mask using binarisation threshold from 0.001 to 0.005, where 0.005 gave warning, the FSC curve has a prominent peak in the FSC plot. I tried changing these parameters and tried the output from other refinement job with bigger box but all give this peak.

my questions
1- What caused and how to get rid of this peak?
2- If this peak problem could not be fixed, can I use proceed with such post-process.star file for ctf refinement and polishing?

Thank you very much for your help and time.

<pastedImage.png>

Last iteration before conversion:

 CurrentResolution= 3.93402 Angstroms, which requires orientationSampling of at least 2.04545 degrees for a particle of diameter 220 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 1305
 OrientationalSampling= 0.46875 NrOrientations= 145
 TranslationalSampling= 0.4605 NrTranslations= 9
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 41760
 OrientationalSampling= 0.234375 NrOrientations= 1160
 TranslationalSampling= 0.23025 NrTranslations= 36
Expectation iteration 25
<pastedImage.png>
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