Hi Remi,
In relion-1.4 this will be easier: you can just start an autorefine from
local searches. In relion-1.3, you need to restart an old run from some
intermediate iteration and modify the model and optimiser.star files of
that iteration to provide the other mask. Just change the value for the
lab with the solvent mask.
HTH,
S

> Dear Sjors,
>
> Thank you very much for your reply.
> I am currently trying something like that. I ran an auto-refine on the
> whole particle. Then I defined a 3D mash around only one of the two
> domains. Then I continued the auto-refine providing this mask to further
> refine this domain only. However, it is not clear to me what option to use
> in relion_refine to force it to continue auto-refine using local search
> only.
>
> Thanks for your help
>
> All the best
>
>
> Rémi Fronzes
> G5 biologie structurale de la sécrétion bactérienne, institut Pasteur
> CNRS UMR 3528, institut Pasteur
>
> Office: +33 (0)145688864
> Lab: +33 (0) 145688863
> Mobile: +33 (0) 688263992
> Email: [log in to unmask] <mailto:[log in to unmask]>
>
> 25 rue du Docteur Roux
> Bâtiment Metchnikoff, 3ème étage
> 75015 Paris, France
>
>> Le 26 févr. 2015 à 09:16, Sjors Scheres <[log in to unmask]> a
>> écrit :
>>
>> Dear Remi,
>> Currently, one would have to do masked refinements of both domains
>> separately (and somehow keep them from mixing up by using local
>> searches).
>> Ongoing work will try to deal with this in a better way, but this
>> project
>> will probably take a while...
>> HTH,
>> S
>>
>>
>>> Dear All,
>>>
>>> Let’s say a protein complex is composed of two domains liked by a
>>> flexible linker. Is there a way to refine each domain independently in
>>> relion ?
>>> For example, if I provide only domain 1 as staring model, will it push
>>> relion to refine this domain over the other ? (given that the two
>>> domains
>>> have sufficiently distinct structures)
>>>
>>> Thanks
>>>
>>> All the best
>>>
>>> Rémi
>>>
>>>
>>> Rémi Fronzes
>>> G5 biologie structurale de la sécrétion bactérienne, institut
>>> Pasteur
>>> CNRS UMR 3528, institut Pasteur
>>>
>>> Office: +33 (0)145688864
>>> Lab: +33 (0) 145688863
>>> Mobile: +33 (0) 688263992
>>> Email: [log in to unmask] <mailto:[log in to unmask]>
>>>
>>> 25 rue du Docteur Roux
>>> Bâtiment Metchnikoff, 3ème étage
>>> 75015 Paris, France
>>>
>>>
>>
>>
>> --
>> 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
>
>


-- 
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