Re: [Pytom-mail] Run localization at specific points

[Dustin M. <dus...@gm...>]

Hi Irene,

Unfortunately there's not a specific script to do this, and I just do it
manually. However, there are many programs
that allow you to make masks by various means, such as shapes in UCSF
Chimera, thresholding and binarize masks
in IMOD, and many other mask making utilities in EMAN2 / RELION / etc.

HTH
___

Cheers,
Dustin M.


On Thu, Jul 12, 2018 at 7:56 AM Irene De teresa <ire...@em...>
wrote:

> Hi Dustin,
>
> Thanks a lot for your answer!
>
> I was looking for a direct solution, since I am interested in doing
> template matching at around 2000 points, rather than the  ~10^8 voxels that
> the full tomogram has...
>
> Is there some script available to do something like this?
>
> Thanks!
> Irene
>
> On Jul 11, 2018, at 4:47 PM, Dustin Morado <dus...@gm...>
> wrote:
>
> Hi Irene,
>
> The best way I know of how to do this is to mask the output scores volume
> before picking peaks.
> You can make a mask by binary thresholding etc. We have done this to
> discard the false peaks we often
> get at the air-water interface by masking out the edges of the score
> volume before peak picking.
>
> HTH
> ___
>
> Cheers,
> Dustin M.
>
>
> On Wed, Jul 11, 2018 at 3:35 PM Irene De teresa <ire...@em...>
> wrote:
>
>> Hello all,
>>
>> I am new in PyTom and I am interested in running a template matching
>> algorithm, but only at very specific points in a tomogram.
>>
>> I was checking how to modify the localization job that is provided by the
>> PyTom tutorial (pytom.org/doc/pytom/tutorial.html), but I couldn’t
>> manage to indicate the list of points at the tomogram where I want to
>> compute the cross-correlation coefficients with respect to the reference
>> particle. Does anyone have an idea of how could I do it?
>>
>> Thanks a lot in advance!
>> Best,
>>
>> Irene
>>
>>
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