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

[Raja Dey]

Hi Takanori,
Thanks for your quick response. Actually I have done it as suggested by
you. The shape of the final map didn't come out as expected. So, I thought
to give a try with 3D reference.  Crystal structure of the same protein
(tetramer) from different origin is available which I used to create the
reference.
best regards,
Raj

On Wed, Feb 12, 2020 at 10:00 AM Takanori Nakane <tnakane at mrc-lmb.cam.ac.uk>
wrote:

> 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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> > 3dem at ncmir.ucsd.edu
> > https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
> >
>
>
>
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