This package contains an EMC and a Difference map implementation for simS2E/SIMEX.
start_orient
compile_EMC
EMC.c
runEMC.py
make_diagnostic_figures.py
[dir]quaternions
[dir]supp_py_modules
gcc, cmath library
Python2.7
Cython
openmp
Use start_orient to automatically start the EMC module in simS2E. Here's a summary of what start_orient does ./start_orient - uses "compile_EMC" to compile EMC.c into executable "EMC" - uses "compile_EMC" to compile Cython files in supp_py_modules - starts orientation recovery with Python script "runEMC.py" runEMC.py - converts h5 diffraction data to sparse photon.dat in tmp dir. - also creates detector.dat in tmp dir. - uses EMC executable iteratively and saves output in tmp dir. - returns simS2E standard output in orient_YYYY_MM_DD_hh_mm_ss.h5
Modify "start_orient" to customize orientation recovery. Here are some options, in brief
The file directories should almost certainly be modified: SRC: Location of source code for reconstruction (e.g. EMC.c runEMC.py) INPUT: Location of input data (diffraction images upstream along simS2E) TMP: Where intermediate EMC output should be stored OUTPUT: Where output should be stored for the next step in simS2E
Other options include: INITIALQUAT: starting level for quaternion refinement MAXQUAT: final level of quaternion refinement MAXITER: maximum number of EMC iterations for intensity reconstruction MINERR: (in quotes) the change in 3D model between iterations below which either a finer rotation group sampling is chosen or EMC iteration terminates if no finer sampling is available BEAMSTOP: 0 for no beamstop, 1 for circular plus strip beamstop PLOT: model error and convergence plots generated as EMC iterates DETAILED: (caution: consumes much disk storage) outputs intermediate 3D volumes of the reconstruction SLEEPDUR: number of seconds to pause between reconstructions NUMRECON: number of independent EMC reconstructions to attempt
For other options, compare the fields in start_orient with the usage help from: python runEMC.py -h
start_phasing
compile_DM
object_recon.c
runDM.py
gcc, cmath library
fftw
Python2.7
Use start_phasing to automatically start the phasing module in simS2E. Here's a summary of what start_phasing does ./start_phasing - uses "compile_DM" to compile object_recon.c into executable "object_recon" - uses "runDM.py" to start iterative phase retrieval. runDM.py - computes a crude initial support based on 2-means clustering of the autocorrelation function - saves crude initial support to support.dat - starts shrink_wrap + iterative phase retrieval using this support and other parameters (listed below) - saves intermediate output to file
Modify "start_phasing" to customize iterative phase retrieval. Here are some options, in brief
The file directories should almost certainly be modified: SRC: Location of source code for phasing (e.g. object_recon.c runDM.py) INPUT: Location of input 3D diffraction volume TMP: Where intermediate phasing output should be stored OUTPUT: Where output should be stored simS2E
Other options include: NUMTRIALS: number of random restarts for each support size STARTAVE: support averaging starts after these many iterations for each randomly restarted reconstruction trial LEASH: leash parameter for the modified difference map SHRINKCYCLES: number of times to run the shrink_wrap support-shrinking algorithm SLEEPDUR: number of seconds to pause between reconstructions NUMRECON: number of independent phasing reconstructions to attempt
For other options, compare the fields in start_phasing with the usage help from: python runDM.py -h