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

[Irene De t. <ire...@em...>]

Thank you for your reply, Dustin!
I will check those possibilities.

Cheers,
Irene


> On Jul 16, 2018, at 10:08 AM, Dustin Morado <dus...@gm...> wrote:
> 
> 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
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Pytom-mail mailing list
>>>> Pyt...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/pytom-mail