- Limitations and scope of MOTIF-EM
- 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.
- There is a learning curve to use the software and patience is required. The best way to start is to follow the example testcase
- 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)
- The software runs on a computing cluster of many nodes
- 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.
- Download and unpack the MOTIF-EM.
- 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
- 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).
- 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.
- Setting paths and linking libraries
- 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:$PATH”.
- Make sure the paths of installed intel lapack runtime libraries are included in the system runtime library path. For example in my computer, the intel libraries are stories at “/usr/local/motifEM/intel”, so I do: “setenv LD_LIBRARY_PATH /usr/local/motifEM/intel/mkl/9.1.023/lib/em64t:$LD_LIBRARY_PATH” or “export LD_LIBRARY_PATH=/usr/local/motifEM/intel/mkl/9.1.023/lib/em64t:$LD_LIBRARY_PATH”
- Make sure MPI installation is also properly linked. For example, in my computer MPI is installed as “/usr/local/motifEM/mpich2-1.3.2p1/”, so I do: “setenv PATH /usr/local/motifEM/mpich2-1.3.2p1/bin:$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”).
- 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
- To run MOTIF-EM on a testcase follow the commands in run_commands.html. Check example.html for an example testcase.
- 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.