Classification example: Difference between revisions
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= 10,000 70S ribosomes wi/wo EFG = | |||
The test data set that will be used below was provided by Joachim Frank and is stored at the EBI-EMDB. | |||
== Download data and reference == | == Download data and reference == | ||
Download the test data set | Download the test data set from [http://www.ebi.ac.uk/pdbe/emdb/singleParticledir/SPIDER_FRANK_data/J-Frank_70s_real_data.tar here], as well as the corresponding metadata that is stored in [http://www.ebi.ac.uk/pdbe/emdb/singleParticledir/SPIDER_FRANK_data/J_FRANK_70S_REAL/Ribosome_information_01_13_09.pdf this PDF file]. Save both files in your working directory. | ||
[ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1056/map/emd_1056.map.gz EMDB entry 1056] will be used as initial reference. Save this file in the same working directory. Note this reference has the same pixel size (2.8A) and the same box size (130x130) as the data set above. Therefore, no re-scaling or windowing operations are necessary. | |||
Unpack the data as follows: | Unpack the data as follows: | ||
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mv emd_1056.map emd_1056.mrc | mv emd_1056.map emd_1056.mrc | ||
== Prepare the input STAR file == | == Prepare the input STAR file == |
Revision as of 12:54, 5 October 2011
10,000 70S ribosomes wi/wo EFG
The test data set that will be used below was provided by Joachim Frank and is stored at the EBI-EMDB.
Download data and reference
Download the test data set from here, as well as the corresponding metadata that is stored in this PDF file. Save both files in your working directory.
EMDB entry 1056 will be used as initial reference. Save this file in the same working directory. Note this reference has the same pixel size (2.8A) and the same box size (130x130) as the data set above. Therefore, no re-scaling or windowing operations are necessary.
Unpack the data as follows:
tar -xf J-Frank_70s_real_data.tar gunzip emd_1056.map.gz mv emd_1056.map emd_1056.mrc
Prepare the input STAR file
From the PDF provided by Joachim Frank select the following (14) lines and save them in a text file called defocus.dat
1 3 1347.0 1347.0 21580. 2 3 505.00 1852.0 24833. 3 3 989.00 2841.0 26450. 4 3 857.00 3698.0 28320. 5 3 475.00 4173.0 30993. 6 3 349.00 4522.0 33150. 7 3 478.00 5000.0 34588. 8 3 1242.0 6242.0 21580. 9 3 713.00 6955.0 24833. 10 3 1255.0 8210.0 26450. 11 3 1022.0 9232.0 28320. 12 3 304.00 9536.0 30993. 13 3 232.00 9768.0 33150. 14 3 232.00 10000. 34588.
Then save the following lines as a file called make_star.csh
#!/usr/bin/env csh
ls -l win/*dat | awk '{print $NF}' >imagelist
#
relion_star_loopheader rlnImageName rlnMicrographName rlnDefocusU rlnVoltage rlnSphericalAberration rlnAmplitudeContrast > all_images.star
#
set ngr = 14
set gr = 0
while ($gr < $ngr)
@ gr++
set nn=`head -n $gr defocus.dat | tail -1 | awk '{print int($3)}'`
set tot=`head -n $gr defocus.dat | tail -1 | awk '{print int($4)}'`
set def=`head -n $gr defocus.dat | tail -1 | awk '{print $5}'`
head -n ${tot} imagelist | tail -n ${nn} |awk -v"def=$def" -v"gr=$gr" '{print $1, gr, def, 200, 2, 0.1}' >> all_images.star
end
And execute it to generate the input STAR file with all image names and CTF information, using the command:
csh make_star.csh