[3dem] question in post-processing

[Mohamed A Sayed]

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.


[cid:856f3e94-8d33-4343-b90c-0da81494cd59]


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

[cid:57a88797-0fb0-4e26-8cc9-aca291667ea6]
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200503/7801eae1/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: pastedImage.png
Type: image/png
Size: 47999 bytes
Desc: pastedImage.png
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200503/7801eae1/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: pastedImage.png
Type: image/png
Size: 17333 bytes
Desc: pastedImage.png
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200503/7801eae1/attachment-0003.png>