If you get stuck anywhere, email us.

At this point, we assume you have downloaded and compiled MOTIF-EM as per http://ai.stanford.edu/~mitul/motifEM/compiling.html

Make sure you have followed the instructions under “Setting paths and linking libraries” in the above link.

Do these in the front-node of your computing cluster:

-1- go to the directory in which you want to work

-2- store the two cryo-EM maps here. They should be in XPLOR format. Limit their sizes to 100x100x100 Å3 .

-3- generate parameter files

generate_params.MPI.pl <MOTIF-EM source directory> <map.1.xplor> <map.2.xplor>

-4- finally run MOTIF-EM

- Run the following two commands sequentially in your cluster:

mpiexec -n <numprocs> motifem.svds.kps

mpiexec -n <numprocs> motifem

-- where <numprocs> is the number of processors you want use

-- make sure all the intel libraries are properly linked and also the essential directories as described in the installation page http://ai.stanford.edu/~mitul/motifEM/compiling.html under “Setting paths and linking libraries”.

For example, this is a typical job file I use to run the above in my computing cluster.

-5- Now many candidate will be generated. To analyze one of them:

analyze_results.pl <which_result>

If you want to analyze the 1st candidate enter 1 for <which_result>, and so on.

This will generate the conserved domain map pair as two *dom*.xplor files. *dom*.comp.xplor are the remnant maps after extracting the domains from the input map pair.

You may view them using chimera.

-6- Optional: Finally clean up the working directory by running “clean.pl”

Expected output files:

If step 3 is successful, you should see a “inp.txt” file in the working directory. This is a typical inp.txt file.

If step 4 is successful, you should see a file “top50.txt” in the working directory.