[3dem] [EXTERNAL] Re: About over-estimation

[Frank, Joachim]

I was NOT suggesting to run an FSC between one of the constituent maps and its counterpart in the model. I was suggesting to simply report the resolutions of the constituent maps and be done with it. J

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From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Basil Greber <basilgreber at gmx.net>
Sent: Friday, May 21, 2021 5:12:26 AM
To: Jay Rai <jrai at fsu.edu>
Cc: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: [EXTERNAL] Re: [3dem] About over-estimation

Hi,

That model vs. map FSC does not look normal. You should be rather skeptical of this outcome.

Basil


Am 20.05.2021 um 19:33 schrieb Jay Rai <jrai at fsu.edu<mailto:jrai at fsu.edu>>:

Thank you for your suggestion.
Yes, I did same.  out of curiosity -i can still use chimeric maps for model refinement, right?
In my case, I use it for phenix real space refinement. Since, I need to provide the resolution, I provide the resolution from the largest maps. I found out that map to model resolution is somewhat acceptable (0.5). I have attached the map to model fsc too.
Thank you once again.

With kind regards,
Jay Rai​

Jay Rai, Ph.D.
Assistant in Research
Florida State Universit
Institute Of Molecular Biophysics
Email: jrai at fsu.edu<mailto:jrai at fsu.edu>
Twitter: @nepalijamesbond


________________________________
From: Frank, Joachim <jf2192 at cumc.columbia.edu<mailto:jf2192 at cumc.columbia.edu>>
Sent: Thursday, May 20, 2021 2:03 PM
To: Jay Rai <jrai at fsu.edu<mailto:jrai at fsu.edu>>; 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu> <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>; 3dem <3dem-bounces at ncmir.ucsd.edu<mailto:3dem-bounces at ncmir.ucsd.edu>>
Subject: RE: About over-estimation

After stitching there is no way to determine the resolution – you have introduced sharp boundaries that will lead to incorrect estimation of resolution.  Why not simply report the resolutions of the individual maps that you have used to produce the chimeric structure?



--Joachim



From: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Jay Rai
Sent: Thursday, May 20, 2021 1:59 PM
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>; 3dem
Subject: [EXTERNAL] [3dem] About over-estimation





Dear Cryo EM folks,
I am just curious..
I focus refine each subunit of maps seperately. Then I used chimera's vop maximum to stich the map.
But when I refine that map to model, it is showing my resolution 2 angstrom.
I even take the unfiltered map from each subunits and stich and so the relion_preprocess and again same resolution.
I know it is because of the noise from each maps (which are outside the mask). I stick the maps from multi body refinement and it is ok so it must be the noise that makes the resolution higher.
Is there any way to calculate the resolution? Or in other words, is there any way to create the composite map?
Any help is greatly appreciated.



With kind regards,
Jay Rai​









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