[3dem] Autopick in relion 3.06 using 3D reference

[Takanori Nakane]

Hi,

I don't know. It is a black box and I don't use it.

Best regards,

Takanori Nakane

On 2020/02/12 20:13, Clara Kielkopf wrote:
> Takanori,
> Do you have similar reservations about reference-based particle picking 
> in Cryosparc?
> Many thanks,
> -Clara
> 
>     Message:
>     Date: Wed, 12 Feb 2020 16:00:45 -0000
>     From: "Takanori Nakane" <tnakane at mrc-lmb.cam.ac.uk
>     <mailto:tnakane at mrc-lmb.cam.ac.uk>>
>     To: "Raja Dey" <rddey80 at gmail.com <mailto:rddey80 at gmail.com>>
>     Cc: 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
>     Subject: Re: [3dem] Autopick in relion 3.06 using 3D reference
>     Message-ID:
>             
>     <5bf02f0ee0bad565b4d4fcb5f87b2f69.squirrel at mail.mrc-lmb.cam.ac.uk
>     <mailto:5bf02f0ee0bad565b4d4fcb5f87b2f69.squirrel at mail.mrc-lmb.cam.ac.uk>>
>     Content-Type: text/plain;charset=iso-2022-jp
> 
>     Hi,
> 
>     I don't recommend this. I always start by picking
>     about 10K - 100K particles by Laplacian-of-Gaussian picker
>     (this is very quick) and running Class2D to make a
>     template.
> 
>     A 3D map from a PDB file does not necessarily match
>     the absolute grey scale of the micrographs. It might work,
>     but not always.
> 
>     Best regards,
> 
>     Takanori Nakane
> 
>      > Dear Members,
>      > I am trying to pick particles using a 3D reference created from a
>      > published
>      > pdb file. I followed these steps to create the reference.
>      > 1. used chimera to create a 15A mrc file from the pdb file.
>      > 2. used relion image handler to change the pixel size (equal to the
>      > micrographs) and box size (approximately double the particle size).
>      > 3. So far, no particle has been picked up after multiple trials
>      > 4. Then I ran the same job as a control on tutorial data of beta
>      > galatosidase and unfortunately no success.
>      >
>      > Don't know what I am missing. If anyone got success and have
>     experience on
>      > running autopicking job in relion3 using 3D reference, sharing your
>      > knowledge would be very helpful.
>      >
>      > Thanks and have a wonderful day.
>      >
>      > Raj
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> 
> 
>     End of 3dem Digest, Vol 150, Issue 22
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