Hi Wei,
Increasing the number of cores will not make the expansion of the movie
frames faster.
You could try the script at the bottom of this message. It will take the
subset of 90k x 22 movie frames from the original particles_movie.star
file, which contains 220kx22 movie frames. This should speed up the
expansion. Still, it will take quite a few hours.
HTH,
S
#!/usr/bin/env csh
#
if ($# != 3) then
echo ' Usage: ' $0 ' run1_data.star particles_movie.star
particles_movie_selected.star'
echo ''
echo ' Where run1_data.star is a selection of an originally larger
data set of the averaged particles.'
echo ' The input particles_movie.star contains the movie frames of
the entire larger data set.'
echo ' The output particles_movie_selected.star will contain the
movie frames only for those particles in run1_data.star.'
echo ' Using particles_movie_selected.star in a continuation of run1
will speed up the expansion of the movie frames.'
else
set star_selected_particles=$1
set star_all_movies_frame=$2
set star_selected_movie_frames=$3
awk '{if (NF > 3) exit; print }' < ${star_all_movies_frame} >
${star_selected_movie_frames}
relion_star_printtable ${star_selected_particles} data_
rlnMicrographName | sort | uniq | sed 's|.mrc||' > mics.dat
relion_star_printtable ${star_selected_particles} data_ rlnImageName >
parts.dat
foreach m (`cat mics.dat`)
grep $m ${star_all_movies_frame} > mics_part.dat
grep $m parts.dat > parts_mic.dat
foreach p (`cat parts_mic.dat`)
grep ${p} mics_part.dat >> ${star_selected_movie_frames}
end
echo -n "."
end
echo " "
echo "done!"
endif
--
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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