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

[Clara Kielkopf]

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>
> To: "Raja Dey" <rddey80 at gmail.com>
> Cc: 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>
> 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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