Hi,
This depends on the target: what fraction of the molecule
is flexible? What is the resolution of the rigid and flexible regions?
This point was discussed in this mailing list before; please study
the archive.
My default strategy is to perform Polishing on consensus refinement
before extensive classification and subtraction but admittedly
I don't work on very flexible proteins.
Best regards,
Takanori Nakane
On 2020/12/26 19:50, Ahmad Khalifa wrote:
> Hi Takanori,
>
> I have a related question. What if part of my molecule is really flexible? In this case performing bayesian polishing on the more rigid part after
> subtraction should capture the true motion of the entire particle, no? Unless you mean that the way bayesian polishing is implemented does not account
> for subtracted particles, in this case, would passing a postprocess star file with a mask centered on the more rigid part of the particle be an
> acceptable compromise?
>
> Best regards.
>
> On Fri, Dec 25, 2020 at 1:27 PM Takanori Nakane <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Hi,
>
> You cannot perform Bayesian Polishing on subtracted maps.
>
> Your particles in raw movies are "full", while your reference maps
> are subtracted. The comparison is not consistent.
>
> Best regards,
>
> Takanori Nakane
>
> On 2020/12/25 19:02, Shanti Pal Gangwar wrote:
> > Hi All,
> > I am doing a focused refinement on the subtracted particles.
> > 3D Refinement and CTF refinement (Beam Tilt/Defocus) on these subtracted particles improved the map significantly. However, Bayesian Polishing
> > followed by 3D refinement did yield an extremely poor quality map (resolution dropped 2X). Any help would be appreciated.
> >
> > All the processing steps were done in RELION 3.1.
> > Happy Holidays.
> >
> > Best
> > Shanti Pal
> >
> >
> >
> >
> >
> >
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