Hi Ludo,
The program relion_run_ctffind has an --only_make_star that will remake
the STAR file for you without having to rerun CTFFIND3. That will help
in option 1). Another possibility would be to extract the movie
particles using relion-1.2, and only after that move to relion-1.3.
Nothing has changed in the particles.star files.
HTH, S
On 07/17/2014 03:40 PM, Ludovic Renault wrote:
> Hi Sjors,
> I have somewhat a similar issue as Edoardo.
> I processed data with 1.2 relion. Data has been collected as movies.
> Now I would like to extract movies.
>
> 1) But in 1.2 the process was a bit different.
> I didn't use a micrograph list with ctf imformation to extract my
> particles.
> Should I re-create a micrographs.star with micrograph inspection,
> re-run ctf estimation to get the micrographs_ctf.star and re-create my
> big initial stack keeping same star file name I had originally so my
> selected subset is usable?
>
> 2) Another option is to extract the coordinates from my subset and
> restart a 1.3 relion project.
>
> Is option 1 the way to do it?
> Thanks,
> Ludo
>
>
> On Tue, Jul 1, 2014 at 2:47 PM, Sjors Scheres
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Hi Eduardo,
> Yes that's right: that script has been removed and I will remove
> the mention of it from the Wiki.
> This is now done throught the "Micrograph inspection" job-type on
> the GUI. As an input you can use the linux wildcard, and then you
> can save a STAR file with all the mics. However, re-extraction
> wouldn't be necessary from 1.2-> 1.3. The same particle stacks and
> particle STAR files should still be valid.
> HTH,
> S
>
>
> On 07/01/2014 01:43 PM, Edoardo D'Imprima wrote:
>
> Dear Sjors,
>
> I'm trying to run Relion 1.3 using the dataset that was
> processed with Relion 1.2. Since I already performed ctf
> correction I just need to extract the particles but the
> program is asking for the micrograph.star file. If I use a
> wildcard from the GUI to define which data to extract (*.mrc)
> it complains saying that the input should be in .star file.
> Is there any procedure that we can use to address this point?
> I've see on the wikipage the command
> relion_star_all_micrographs but is not present in our compiled
> program list of Relion 1.3.
>
> Many thanks,
>
> Edoardo
> ---------------------------------------------------
> Edoardo D'Imprima
> PhD Student
> Max Planck Institute of Biophysics
> Structural Biology Department
> Max-von-Laue Straße 3
> 60438 Frankfurt am Main
> Germany
>
> Tel: +49 (0) 69 6303 3015
>
>
> --
> 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
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