FAQs: Difference between revisions
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The following awk command may be used to select images belonging to classes number 3 or 4 (assuming rlnClassNumber is the 13th column): | The following awk command may be used to select images belonging to classes number 3 or 4 (assuming rlnClassNumber is the 13th column): | ||
<code> | <code> | ||
awk '{if (NF= | awk '{if (NF<= 2) {print} else {if ($13==3 || $13==4) print }}' < classify_it000025_data.star > class3_only_input.star | ||
</code> | </code> | ||
Some knowledge of awk is REALLY useful! [http://www.hcs.harvard.edu/~dholland/computers/awk.html This light awk introduction] may be helpful. The command above prints all lines if the number of fields (NF) is 1 (i.e. for the header), and else (i.e. for the data block) it will only print those lines if the 13th column ($13) equals 3. Note one may change the "==" signa for ">", "<=", etc. That way, one could select images above a certain MaxValueProbDistribution, within a certain AnglePsi range, etc. | Some knowledge of awk is REALLY useful! [http://www.hcs.harvard.edu/~dholland/computers/awk.html This light awk introduction] may be helpful. The command above prints all lines if the number of fields (NF) is 1 (i.e. for the header), and else (i.e. for the data block) it will only print those lines if the 13th column ($13) equals 3. Note one may change the "==" signa for ">", "<=", etc. That way, one could select images above a certain MaxValueProbDistribution, within a certain AnglePsi range, etc. | ||
Revision as of 09:01, 30 July 2012
Preprocessing
Do I need to downsize my images?
RELION will estimate the resolution of your model and downsize the images internally. Therefore, using downsized images will NOT be (much) faster than using large images. In general it is therefore NOT recommended to use downsized images: it could limit your resolution. The only reason why one would want to downsize images if they are too big (e.g. 800x800 pixels) for the reconstruction(s) to fit into memory. The program will complain about that.
3D refinement
How can I make a plot of the orientational distribution of my particles?
RELION outputs all the information in the STAR files for each iteration, but at the moment will not make a plot of this. You can use the make_orientational_distribution_plot.csh script to make a BILD file (using XMIPP), which can then be read into UCSF Chimera.
Classification
Do you have an example of how to run 3D classification?
Yes, see the Classification example.
Should I refine my 3D classes in a different program to reach higher resolution?
This is not necessary: you may do so in RELION. Higher resolution often means using fine orientational and translational samplings, which may be prohibitive (speed and memory-wise) inside classification runs. One can however write out a new STAR file that contains only the images belonging to a certain class (see the next FAQ). That STAR file could then be used for a single-reference refinement with fine samplings in RELION.
How can I select images from a STAR file?
The following awk command may be used to select images belonging to classes number 3 or 4 (assuming rlnClassNumber is the 13th column):
awk '{if (NF<= 2) {print} else {if ($13==3 || $13==4) print }}' < classify_it000025_data.star > class3_only_input.star
Some knowledge of awk is REALLY useful! This light awk introduction may be helpful. The command above prints all lines if the number of fields (NF) is 1 (i.e. for the header), and else (i.e. for the data block) it will only print those lines if the 13th column ($13) equals 3. Note one may change the "==" signa for ">", "<=", etc. That way, one could select images above a certain MaxValueProbDistribution, within a certain AnglePsi range, etc.