RafaUsefulScripts

Rafa's Useful Scripts

Kerdensom

Select the interesting part of the images using xmipp_xmask; convert to data-format; calculate a 5x5 kerdensom; convert back to image format; and display the som.

xmipp_xmask -img selfile.med.xmp
xmipp_img2data -sel selfile.sel -mname mask.spi -fname selfile.dat
xmipp_kerdensom -din selfile.dat -cout selfileker -xdim 5 -ydim 5 -reg0 500 -reg1 100 -steps 5 -verb 1
xmipp_data2img -sel selfileker.sel -iname selfileker.cod -mname mask.spi
xmipp_show -som selfileker

Submitting a mpi job in jumilla

bsub -q 1week_parallel /home/bioinfo/bioinfo/MPICH/bin/mpirun -np 10 -machinefile ~/machines.dat \
 `which xmipp_mpi_MLalign2D` -i img.sel -nref 10 -fast -o ML10ref

It requires a file ~/machines.dat containing the name of the nodes:

rueda.cnb.uam.es
ribera.cnb.uam.es
ribeiro.cnb.uam.es
rioja.cnb.uam.es
cartojal.cnb.uam.es

Create Masks from a map

xmipp_threshold -i vol.xmp -o vol.bin -binarize -below "threshold"
xmipp_separate_objects -i vol.bin -o vol

Check the volumes to find the adecuate mask

You can modify the mask with the following program

xmipp_morphology -i vol?????.bin -o vol?????dil.bin -dil

or

xmipp_morphology -i vol?????.bin -o vol?????ero.bin -ero

Apply the mask

xmipp_mask -i vol.xmp -o vol_mask.xmp -mask vol?????.bin

USER's COMMENTS

If you have any suggestion, please use this form!	Main.SjorsScheres	12 Dec 2006 - 11:44
Comments will be displayed just above this form	Main.CarmenSanMartin	12 Dec 2006 - 12:24

-- Main.RafaelNunezRamirez - 05 Jan 2007