Run
Run the fitting
fit.py efitter_params.py
The fitting runs will execute in the background and take from a few dozens of minutes to several hours depending on the case.
In the output, you should have got the following directory structure:
master_outdir/ # Directory specified with "master_outdir" parameter in params.py config_prefix1/ # named after config_prefix specifications in fitmap_args in params.py map1.mrc/ # named after the filenames of the EM maps used map1.mrc # symbolic link to the reference map pdb_file_name1.pdb/ # named after the pdb file names used for fitting solutions.csv # the list of solutions and their scores log_err.txt # standard error log log_out.txt # standeard output log run.sh # sbatch script used for running the job ori_pdb.pdb # symbolic link to the original query file map1.mrc # symbolic link to the reference map pdb_file_name2.pdb/ pdb_file_name3.pdb/ config.txt # A config file for fitting, saved FYI. map2.mrc/ config_prefix2/ config_prefix3/
Note
The fitting is complete when each of the
.pdb
directories containssolutions.csv
file.Inspect the
log_out.txt
files for status andlog_err.txt
for error messages.Upon completion, calculate p-values:
genpval.py <fitting directory/master_outdir>
This should create additional files in each
.pdb
directory:Rplots.pdf solutions_pvalues.csv
The
solutions_pvalues.csv
is crucial for the global optimization step.