Dear Julian,
Hopefully our most recent chapter in Meth Enzym will help.
http://dx.doi.org/10.1016/bs.mie.2016.04.012
Indeed, it is the 'Reference mask' option that is needed, possibly
together with the subtraction jobtype.
For making masks, you can use relion_mask_create, but we also often use
other software (e.g. volume eraser in Chimera, a fitted PDB-file, etc)
HTH,
Sjors
On 12/05/2016 01:10 PM, Julian Reitz wrote:
> Hi all,
>
> we would like to do some 3D-classifications of our data.
> However we have reasons to believe, that there are positions in the structure that show independent heterogeneity. Meaning, that it is difficult to cover this variety with a normal classification.
>
> We would like to do something as follows:
> We would like to apply a mask that masks out a single of this regions and that the classification (and the following refinement) puts the focus on this region.
>
> As far as there is no misunderstanding on my site this is not what the "Reference mask" option for 3D-Classification is made for, since it should be used to mask out protein against the solvent.
>
> Any suggestions about how to do this?
>
> Best,
> Julian
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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