[3dem] Large image box size in CryoSparc2 and Relion3

[Takanori Nakane]

Hi,

> I do not want to coarsen them.

Really? For Class2D, you don't need high resolution at all.
Down-sampling to 3.5 A / pix is the best way forward.

For Refine3D, you should specify "Skip padding: Yes". With this option,
we have successfully refined a 1024 px box using GTX 1080 Ti (11 GB / GPU).

Best regards,

Takanori Nakane

> Hi Everybody,
>
> I wonder if you can help me, any suggestions are welcome:
>
> We need to process particles that are big enough and fit only in the
> boxes of the size 900x900. I do not want to coarsen them.
>
> Is there any way I can process them in CryoSparc (ver 2), or Relion 3?
> So far? CryoSparc2 crashes at 2D classification complaining that :
> *cufftAllosFailed*
>
> If I want to have 100? or 20 classes it fails in ~5min, with 5 classes
> it failed after iteration #19. The error message is the same.
>
> Relion 3 was more efficient: running two (2) month for 50 classes?
> reaching the iteration #2. Then the guy was mercilessly killed.
>
> I am using 4 GPU with the memory of ~ 12Gb each
>
> Set consists of ~ 35 000 images.
>
> Many thanks in advance. Elena
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Elena Orlova
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck,  University of London,
> Malet Street,
> LONDON  WC1E 7HX
> Tel: (+44) (0)20 7631 6845
> Fax: (+44) (0)20 7631 6803
> e-mail: e.orlova at mail.cryst.bbk.ac.uk
>
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