Dear Sjors,
thank you for your answer. Indeed the chapter in Meth Enzym was from
great help.
But I figured out a problem for our case that for me seems to be more severe.
We are working on a helical reconstruction.
Considering the relevant parameters we have approx. 22 subunits in our
particle boxes.
If I now mask out a single region in the reference map I only use the
information of one of these 22 subunits per particle. And if I mask
out the region in all the subunits I might have the problem that they
are not all in the same state and that the structural heterogeneity is
not consistent for all subunits in one particle.
What would be your advise to deal with this?
Thanks,
Julian
Zitat von Sjors Scheres <[log in to unmask]>:
> 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
--
Julian Reitz, Dipl.-Biochem.
J.W. Goethe Universität Frankfurt am Main
BMLS - Buchmann Institut for Molecular Life Sciences
Frangakis Group
Max-von-Laue-Str. 15 Raum 1.658, D-60438
Tel: +49 (0)69 798-46429
e-mail: [log in to unmask]
http://fcem.uni-frankfurt.de/em
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