1. Limitations and scope of MOTIF-EM
  1. Limit the input cryoEM map sizes to 1,000,000 cubic Angstrom
  2. There is a learning curve to use the software and patience is required. The best way to start is to follow the example testcase .
  3. It may not work in all cases due to reasons such as: map inaccuracies (which is very common), very low map resolution (say worse than 15A)
  4. The software runs on a computing cluster of many nodes

  1. Download and unpack the MOTIF-EM source code.

  1. Install intel lapack libraries. Preferably use Intel Lapack 9.1.023. You can find a copy here: http://robotics.stanford.edu/~mitul/motifEM/intel.lapack.9.1.023.zip

Set the intel library names & paths correctly in the "Make.config" file (in the unpacked source directory) under “INTEL_MATH_LOC”, "LIBPATH", "ILIBS" (also because, 32 bit processors use different libraries as compared to 64 bit processors).

  1. Make sure MPI (http://en.wikipedia.org/wiki/Message_Passing_Interface) is installed, as MOTIF-EM runs on a computing cluster and does parallel computing. You can also run it on your local computer, but it will be much slower.

  1. Compile and generate executables by doing "make" in:

(1) the MOTIF-EM source directory  

(2) the “utility_codes” sub-directory in the source directory

(3) the “MPI_implementation” sub-directory in the source directory

  1. To run MOTIF-EM on a testcase follow the commands in run_commands.html. Check example.html for an example testcase.

  1. Please email us if you have any question/concern/problem in using MOTIF-EM. If you have a testcase that dosn’t work with MOTIF-EM, and you think it should have worked, please email us with details.