Hey,
>Is this from EPU or SerialEM?
>Is this in floating points or integers?
They are from EPU; I believe they are floating points.
>You can confirm the validity of compression by......
Yes I tried this, some look pretty different. Think something went wrong during compression then.
Would using the --estimate_gain option help?
Cheers,
Dylan
-----Original Message-----
From: Takanori Nakane <[log in to unmask]>
Sent: donderdag 22 april 2021 14:58
To: Noone, D.P. (CCB) <[log in to unmask]>; [log in to unmask]
Subject: Re: [ccpem] Corrupted data during compression?
Hi,
> They are gain corrected K3 movies (.mrc)
Is this from EPU or SerialEM?
Is this in floating points or integers?
You can confirm the validity of compression by:
relion_image_handler --i [log in to unmask] --subtract [log in to unmask] --o diff.mrc relion_image_handler --stats --i diff.mrc
This compares the 10th frame of input.mrc and input.tif.
Do this test on several random frames from several movies. Are they different?
Best regards,
Takanori Nakane
On 2021/04/22 13:05, Dylan Noone wrote:
> Hey,
>
> Thanks for your reply and apologies for the delayed response.
>
>> Are they gain corrected K2 movies written by EPU?
>
> They are gain corrected K3 movies (.mrc)
>
>> Please write the full command you used for compression.
>
> relion_convert_to_tiff --i ./Import/mrcs_all/movies.star --o Tiff/
>
> Kind regards,
> Dylan
>
>
> -----Original Message-----
> From: Takanori Nakane <[log in to unmask]>
> Sent: dinsdag 20 april 2021 16:16
> To: Noone, D.P. (CCB) <[log in to unmask]>; [log in to unmask]
> Subject: Re: [ccpem] Corrupted data during compression?
>
> Hi,
>
> > However, I wanted to compress the frames for storage. As such I used relion_convert_to_tiff to turn my gain corrected mrc files to tiffs.
>
> Are they gain corrected K2 movies written by EPU?
>
> Please write the full command you used for compression.
>
> Best regards,
>
> Takanori Nakane
>
> On 2021/04/20 12:18, Dylan Noone wrote:
>> Hey all,
>>
>> I collected some data and it went to high resolution (sub 3A).
>>
>> However, I wanted to compress the frames for storage. As such I used relion_convert_to_tiff to turn my gain corrected mrc files to tiffs.
>>
>> To check the results I then reextracted my particle coordinates from
>> before on the Tiffs and ran 2D Classification, 3D Classification and a Refinement but the results looked super weird (see attached)!
>>
>> Does anyone have any experience in this or know where this may have gone wrong?
>>
>> Thanks in advance,
>>
>> Dylan
>>
>>
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