Dear Grigory,
If you would use the --ref option with a STAR file containing the
references (take the model_classes table from the last _model.star file
from your previous 2d run), then they would hopefully stay intact. I think
you still need to give --K as well with the correct number of classes.
You can also copy the rlnAnglePsi column of the inut data.star file, and
have a second column called rlnAnglePsiPrior, which will set a fixed prior
on the Psi angles. Then you can still manage the width of the prior
through --sigma_psi.

HTH,S

> Dear Sjors,
>
> I've managed to run 2D classification with a mask and local search in
> "continue" mode. But now I would like to re-classify with different number
> of classes, and this is not possible in continue mode. Is there a way to
> do
> 2D classification starting from previously determined shifts/angles and
> not
> from random ones?
>
> Best regards,
> Grigory Sharov
>
> Institute of Genetics and Molecular and Cellular Biology
> Department of Structural Biology and Genomics
> 1, rue Laurent Fries
> 67404 Illkirch, France
> tel. 03 69 48 51 00
> e-mail: [log in to unmask]
>
>
> On Sat, Aug 17, 2013 at 9:25 PM, Sjors Scheres <[log in to unmask]>
> wrote:
>
>> Hi Reggie,
>> Not really, although you could try to provide a 2D mask and then use
>> very
>> strict local angular searches (effectively prohibiting the particles to
>> move at all). This goes beyond the GUI though: you'll need to add the
>> corresponding command-line arguments yourself. You could try the 3D
>> refinement GUI to see what those arguments should be (they're the same
>> for
>> 2D and 3D).
>>
>> HTH, S
>>
>>
>> > Dear Sjors,
>> >
>> > I have a multi-part complex in which one region is always fuzzy. Is
>> there
>> > a way to have RELION do 2D alignment focused on this fuzzy region?
>> >
>> > Reggie
>> >
>> > --
>> > Reginald McNulty, Ph.D.
>> > Postdoctoral Research Associate
>> > The Scripps Research Institute
>> > Johnson Lab
>> > Department of Integrative Structural and Computational Biology
>> > 10550, N. Torrey Pines Road, MB-31
>> > La Jolla, California 92037
>> > Telephone: 858-784-8652
>> > Cell: 949-436-1263
>> > Email: [log in to unmask]
>>
>>
>> --
>> 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