[3dem] 3dem Digest, Vol 138, Issue 26

[Takanori Nakane]

Hi,

Please don't do that. The GUI prevents you from selecting
these intermediate files.

Only use converged half maps (run_halfX_class001_unfil.mrc) in
PostProcess. The reason is that not all frequencies are included
in the reconstruction during earlier iterations.

If you select 'solvent flattened FSC: Yes' in Refine3D,
FSC values in run_itNNN_halfX_model.star are calculated
from masked maps just as in PostProcess. So you don't need to
run PostProcess on intermediate results.

Best regards,

Takanori Nakane

On 2019/02/11 20:06, Brenda Gonzalez wrote:
> Hi Takanori, yes, I used the non-converged half maps (i.e.
> run_itNNN_halfX_class001_unfil.mrc) for post processing to get those Relion results.
> 
> 
> 
> Brenda Gonzalez
> 
> PhD Candidate
> 
> Department of Biological Sciences – Purdue University
> 
> Purdue SACNAS Chapter President
> 
> AGEP Scholar
> 
> e: gonzalb at purdue.edu
> 
> ________________________________
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> Subject: 3dem Digest, Vol 138, Issue 26
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>     1. Re: unmasked FSC different (Takanori Nakane)
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> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 11 Feb 2019 19:24:31 +0000
> From: Takanori Nakane <tnakane at mrc-lmb.cam.ac.uk>
> To: 3dem at ncmir.ucsd.edu
> Subject: Re: [3dem] unmasked FSC different
> Message-ID: <8343c2ca-8f7c-c6ef-aa93-4e3ac59b1137 at mrc-lmb.cam.ac.uk>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> 
> Hi,
> 
> Didn't you use non-converged half maps (i.e.
> run_itNNN_halfX_class001_unfil.mrc)
> for PostProcesss?
> 
> Best regards,
> 
> Takanori Nakane
> 
> On 2019/02/11 18:57, Brenda Gonzalez wrote:
>> Hello,
>>
>> I was wondering if anyone has noticed issues with their FSC results using Relion.
>>
>> For a while, I have been getting results where my unmasked FSC curve floats above 0. However, when I looked at the model.star file FSC data and plotted that manually, the unmasked FSC curve actually appears to reach 0.
>>
>> Does anyone know what could be causing this or how I could fix it?
>>
>> Thank you,
>>
>>
>>
>> Brenda Gonzalez
>>
>> Department of Biological Sciences ? Purdue University
>>
>> e: gonzalb at purdue.edu
>>
>>
>> _______________________________________________
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