Hi,
You are right, but I still recommend people to always use a map
that would result from the input particles as a reference
to avoid mistakes and confusion. Other programs and/or future versions
might behave differently.
Best regards,
Takanori Nakane
On 2019/09/17 23:06, Daniel Asarnow wrote:
> Hi Takanori,
> Isn't the (subparticle) mask applied already before the first iteration,
> so that the original reference can be used?
>
> Best,
> -da
>
> On Tue, Sep 17, 2019 at 9:00 AM Takanori Nakane
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Hi,
>
> > For running a 3d refinement with partial signal subtracted
> images, can
> > anyone suggest what works better as mask- spherical mask or a soft
> > mask?
>
> Soft mask.
>
> > Also what reference should one use to ensure proper alignment of the
> > signal subtracted particles?
>
> The reference should contain only the volume that remains after
> subtraction.
> The initial low pass filter might have to be weaker (say 10-15 A,
> instead of
> 40 A) but still at much lower resolution than the resolution of the
> region.
>
> > As my area of interest is quite small compared
> > to the whole particle, using a volume reference of only the
> focussed area
> > simply isn't working. Although, running a recontsruction with the
> signal
> > subtracted particle using relion_reconstruct program is giving a
> pretty
> > good volume.
>
> Did you also try local search?
>
> How small is it? Even when it is too small to be aligned, you
> might still be able to improve the density by running Class3D
> without alignment to select a subset of particles that have
> more-or-less the same relative orientation to the larger subtracted
> region, and then refining the unsubtracted particles.
>
> Best regards,
>
> Takanori Nakane
>
> > Thanks in advance!
> >
> > Shirin
> >
> >
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