Installing IMOD on Rocce

Download IMOD from: http://bio3d.colorado.edu/imod

To install on Rocce run these commands:

wget http://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_4.9.3_RHEL5-64_CUDA3.0.sh
chmod a+x imod_4.9.3_RHEL5-64_CUDA3.0.sh
mkdir -p ~/bin/imod
./imod_4.9.3_RHEL5-64_CUDA3.0.sh -dir ~/bin/imod -skip -yes
echo ". /home/$USER/bin/imod/IMOD/IMOD-linux.sh" >> ~/.bash_profile

After finish logout and log back into Rocce and running this command should output like the following:

mrc2tif

Output:

mrc2tif version 4.9.3 
Copyright (C) 1994-2017 by the Regents of the University of Colorado
mrc2tif [options] <mrc file> <tiff name/root>

 Without -s, a series of tiff files will be created with the
 prefix [tiff root name] and with the suffix nnn.tif, where nnn is the z number. 
  Options:
    -s         Stack all images in the mrc file into a single tiff file
    -c val     Compress data; val can be lzw, zip, jpeg, or numbers defined
		 in libtiff
    -q #       Quality for jpeg compression (0-100) or for zip compression (1-9)
    -S min,max Initial scaling limits for conversion to bytes
    -C b,w     Contrast black/white values for conversion to bytes
    -z min,max Starting and ending Z (from 0) to output
    -i #       Initial file number (default is starting Z)
    -j         Output jpeg file instead of tiff
    -p         Output png file instead of tiff
    -r #       Resolution setting in dots per inch
    -P         Use pixel spacing in MRC header for resolution setting
    -T nx[,ny] Output data in tiles of size nx by ny (nx by nx if ny omitted)
    -O #       Override default for parallel tiff compression on whole image
    -t #       Criterion image size in megabytes for processing file in strips
    -o         Write file with old IMOD code instead of libtiff