Hi Liz,
You could look at the precalculated results of the tutorial: there is a
new star file with metadata for each micrograph. You could then emulate
this with your scripts. It's probably faster to realign the movies in
relion3 though.... You will need them on the disk anyway to do the
polishing.
HTH,
Sjors
> Hi all,
>
> I processed my tilted dataset to 4 Angstrom within RELION-3.0 before I
> realized that in order to do Bayesian polishing RELION-3.0 requires motion
> correction to be run within the RELION-3.0 framework. Rather than
> re-process the whole dataset from the beginning, I would much rather find
> a
> way to convert the motion correction log files (I used motioncorr2 from
> UCSF) into the metadata RELION reads in for Bayesian polishing. When I do
> this, it runs to completion without throwing an error, however the values
> that are output during Bayesian polishing don't make sense, and I'm
> guessing I have failed to supply information that's needed. I monitored
> the RAM consumption during the run and I'm not running out of memory or
> anything like that.
>
> This is what output looks like:
>
> micrograph 50 / 70: 225 particles [7372 total]
> micrograph 51 / 70: 57 particles [7429 total]
> micrograph 52 / 70: 242 particles [7671 total]
> micrograph 53 / 70: 191 particles [7862 total]
> micrograph 54 / 70: 45 particles [7907 total]
> micrograph 55 / 70: 192 particles [8099 total]
> micrograph 56 / 70: 234 particles [8333 total]
> micrograph 57 / 70: 88 particles [8421 total]
> micrograph 58 / 70: 12 particles [8433 total]
> micrograph 59 / 70: 66 particles [8499 total]
> micrograph 60 / 70: 2 particles [8501 total]
> micrograph 61 / 70: 122 particles [8623 total]
> micrograph 62 / 70: 207 particles [8830 total]
> micrograph 63 / 70: 38 particles [8868 total]
> micrograph 64 / 70: 161 particles [9029 total]
> micrograph 65 / 70: 261 particles [9290 total]
> micrograph 66 / 70: 202 particles [9492 total]
> micrograph 67 / 70: 177 particles [9669 total]
> micrograph 68 / 70: 94 particles [9763 total]
> micrograph 69 / 70: 182 particles [9945 total]
> micrograph 70 / 70: 268 particles [10213 total]
> done
>
> it: s_vel: s_div: s_acc: fsc:
>
> 0: 0.60000 10000.00000 3.00000 0.000000000000
> 1: 0.60000 10000.00000 3.00000 0.000000000000
> 2: 0.60000 10000.00000 3.00000 0.000000000000
> 3: 0.60000 10000.00000 3.00000 0.000000000000
> 4: 0.60000 10000.00000 3.00000 0.000000000000
> 5: 0.60000 10000.00000 3.00000 0.000000000000
> 6: 0.60000 10000.00000 3.00000 0.000000000000
> 7: 0.60000 10000.00000 3.00000 0.000000000000
>
> good parameters: --s_vel 0x1.3333333333333p-1 --s_div 0x1.38a8p+13 --s_acc
> 0x1.8p+1
>
>
> written to Polish/job073/opt_params.txt
> ==============================================
>
> Pre-processing was handled by Focus, so at the end of data-collection it
> was easy to take the aligned images and the estimated ctf fits and go. It
> would be pretty inconvenient to have to re-align images within RELION. Has
> anyone gotten this to work before?
>
> Any insight into what the problem could be would be very much appreciated.
> Or any advice or help to get the metadata created properly would be
> amazing. Thanks in advance.
>
> Cheers
> Liz Kellogg
>
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--
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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