where is the origin for the defining the center of the focus mask for focus mask classification

5 posts / 0 new

Fri, 01/19/2018 - 09:01

Jrai

HI all,

I am trying to use focus mask for the focused mask classification but I have no idea how to determine/get the sphere X/Y/Z Co-ordinat.

Anyone has any idea

Thanks

Jay

Fri, 01/19/2018 - 10:06

Jrai

I figuredit out mymyself

Fri, 01/19/2018 - 14:21

niko

A description of how to

A description of how to define focus masks can be found here.

Fri, 01/19/2018 - 23:02

(Reply to #3) #4

Jrai

Thanks a lot. Is it possible

Thanks a lot. Is it possible to use different shapes apart from a sphere? e.g. If I want to use a mask on a small subunit (i.e. 40s) of 80s ribosome, then what shape should I use for masking? If I use a small sphere then it is not big enough to mask whole 40s subunit. If I use a big sphere then, it touches the large subunit as well. And I am afraid that masking won't be as effective as it should be. And, I can see that I can only use a sphere shape mask.

My question is should I use a custom mask having a shape of the 40s and then apply sphere? or How do I apply a mask to the shape of 40s subunit?

Thanking you in advance

Jay

Sat, 01/20/2018 - 08:15

(Reply to #4) #5

niko

It sounds to me as if you

It sounds to me as if you would like to use a 3D mask, not a focus mask. These are two different ways of masking. The 3D mask can have an arbitrary shape and is applied to the 3D reference volume before refinement starts. You can create a 3D mask outside of cisTEM and then import it as a Volume Asset and choose it as a mask in the Manual Refine panel. If you would like to know more about how thes etwo masking options are used, please read Abeyrathne et al, 2016 and look at Figure 1— supplement 2 in this paper (the supplement figure is also shown here).

Abeyrathne et al (2016), Figure 1 - Supplement 2

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where is the origin for the defining the center of the focus mask for focus mask classification