1. Limitations and scope of MOTIF-EM
  1. Limit the input cryoEM map sizes to 1,000,000 Å3. Chop larger maps into smaller pieces and work with each piece separately. Also MOTIF-EM accepts maps only in XPLOR file format.
  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
  5. Memory constraints: If MOTIF-EM is needing more RAM than there is in your system, then either allocate more RAM or consider reducing the sizes of one or both the input structure.

  1. Download and unpack the MOTIF-EM.

  1. Install intel lapack libraries. Preferably use Intel Lapack 9.1.023. You can find a copy here: http://cryoem.utmb.edu/motifEM/intel.lapack.9.1.023.zip
  1. 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. Setting paths and linking libraries
  1. Link the directory names “<MOTIF-EM directory>”, “<MOTIF-EM directory>/MPI_implementation/”, “<MOTIF-EM directory>/scripts‘, “<MOTIF-EM directory>/utility_codes” to the system environment variable $PATH. <MOTIF-EM directory> is the directory name for the MOTIF-EM package with full path. For example, in my computer <MOTIF-EM directory> is “/usr/local/motifEM/pattern_matching/”, so I do “export PATH=/usr/local/motifEM/pattern_matching/:/usr/local/motifEM/pattern_matching/MPI_implementation/:/usr/local/motifEM/pattern_matching/scripts:/usr/local/motifEM/pattern_matching/utility_codes:$PATH” or “setenv PATH /usr/local/motifEM/pattern_matching/:/usr/local/motifEM/pattern_matching/MPI_implementation/:/usr/local/motifEM/pattern_matching/scripts:<MOTIF-EM directory>/utility_codes:$PATH”.
  2. Make sure the paths of installed intel lapack runtime libraries are included in the system runtime library path. For example in my computer, the intel libraries are stories at “/usr/local/motifEM/intel”, so I do: “setenv LD_LIBRARY_PATH /usr/local/motifEM/intel/mkl/9.1.023/lib/em64t:$LD_LIBRARY_PATH” or “export LD_LIBRARY_PATH=/usr/local/motifEM/intel/mkl/9.1.023/lib/em64t:$LD_LIBRARY_PATH”
  3. Make sure MPI installation is also properly linked. For example, in my computer MPI is installed as “/usr/local/motifEM/mpich2-1.3.2p1/”, so I do: “setenv PATH /usr/local/motifEM/mpich2-1.3.2p1/bin:$PATH” (or “export PATH= /usr/local/motifEM/mpich2-1.3.2p1/bin:$PATH”) AND “setenv LD_LIBRARY_PATH /usr/local/motifEM/mpich2-1.3.2p1/lib:$LD_LIBRARY_PATH” (or “export LD_LIBRARY_PATH=/usr/local/motifEM/mpich2-1.3.2p1/lib:$LD_LIBRARY_PATH”).

  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.