[3dem] 3dem Digest, Vol 197, Issue 12

Mon Jan 22 15:24:11 PST 2024

hi everyone,

Here's an old thread about a similar issue that you may be useful:

https://urldefense.com/v3/__https://groups.google.com/g/warp-em/c/-fOnQ34VMO8/m/g8d6C8T6AwAJ__;!!Mih3wA!DjqAEJuLRHCYEMYf4NWvbX3ZaR-2DesLV6_iInT410Cur0dvxFJ_ahzKukPYC_MSF8UjdrTsxHQ2MNS_Dd2Nvxa0$ 

Cheers,
Digvijay

On Mon, Jan 15, 2024 at 2:49 AM Qiang Guo <guoq.tiger at gmail.com> wrote:

> Dear Philipp,
>
> We have a similar issue with Motioncor 2 and Warp when reading the gain
> file, it is a TIF format file, and converting it to MRC format solves the
> issue.
>
> Best,
> Q
>
>
>
>
> <3dem-request at ncmir.ucsd.edu> 于2024年1月11日周四 18:58写道：
>
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>> Today's Topics:
>>
>>    1. Question regarding eer .gain files and defects
>>       (Philipp Sebastian Erdmann)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 11 Jan 2024 10:57:29 +0000
>> From: Philipp Sebastian Erdmann <philipp.erdmann at fht.org>
>> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
>> Subject: [3dem] Question regarding eer .gain files and defects
>> Message-ID: <E489D09B-F277-44DF-9C5C-C0F7BCE1C96A at fht.org>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear All,
>>
>> I recently tried reading the defects from the .gain file of our Falcon4i.
>>
>> However, the xml embedded in the .gain reads as:
>>
>> <defects><!-- Defects file not present --></defects>
>>
>> Is the is bug in the software? Maybe it is not yet implemented by TFS?
>>
>> Are there other ways to extract it?
>>
>> I know the .gain zeros are the defects, but is this not an issue if you
>> take the reciprocal?
>>
>> 1/0 = ?
>>
>> We?re trying to figure out which software does best in processing .eer
>> files of tomograms.
>>
>> (Low dose; ca 3 e/?2)
>>
>> Relion looks perfect but does not produce 1/2 stacks for denoising.
>>
>> Warp and MC3 produce 1/2 stacks, but I can see artifacts in the pixel
>> substitution.
>>
>>
>> Thanks for your help!
>>
>>
>> Philipp.
>>
>>
>> Philipp Sebastian Erdmann
>> Research Group Leader
>> Erdmann Group,
>> Structural Biology Research Centre
>> Human Technopole
>> Palazzo Italia
>> Viale Rita Levi Montalcini, 1
>> 20157 Milan, Italy
>> M. +39 3452453710
>> E. philipp.erdmann at fht.org
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>> ------------------------------
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>> Subject: Digest Footer
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>> ------------------------------
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>> End of 3dem Digest, Vol 197, Issue 12
>> *************************************
>>
>
>
> --
> Qiang (John) Guo
> Department of Molecular Structural Biology
> Max Planck Institute of Biochemistry
> Am Klopferspitz 18
> 82152 Martinsried
> Germany
> Email: guoq.tiger at gmail.com
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-- 

Digvijay Singh, PhD
K99 & Damon Runyon Fellow
Elizabeth Villa Group
University of California, San Diego
https://urldefense.com/v3/__http://www.digvijay.org__;!!Mih3wA!DjqAEJuLRHCYEMYf4NWvbX3ZaR-2DesLV6_iInT410Cur0dvxFJ_ahzKukPYC_MSF8UjdrTsxHQ2MNS_DeK8UQXe$ 
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