swamp-mr options¶

SWAMP-MR: Contact assisted fragment based molecular replacement

usage: swamp-mr [-h] [-workdir [WORKDIR]]
                [-max_concurrent_procs [MAX_CONCURRENT_PROCS]]
                [-max_array_size [MAX_ARRAY_SIZE]]
                [-pdb_benchmark [PDB_BENCHMARK]] [-platform [PLATFORM]]
                [-environment [ENVIRONMENT]] [-extend_solution]
                [-queue [QUEUE]] [-mtz_phases [MTZ_PHASES]]
                [-job_kill_time [JOB_KILL_TIME]]
                [-ncontacts_threshold [NCONTACTS_THRESHOLD]]
                [-consco_threshold [CONSCO_THRESHOLD]]
                [-python_interpreter [PYTHON_INTERPRETER]]
                [-combine_searchmodels] [-use_centroids] [-use_cores]
                mtzfile fastafile conpred sspred

Positional Arguments¶

`mtzfile`	MTZ file with the reflection data
`fastafile`	FASTA file with the sequence of the structure
`conpred`	Residue contact prediction for the target structure
`sspred`	Secondary structure prediction for the target protein

Named Arguments¶

`-workdir`	Working directory to perform MR
`-max_concurrent_procs`
	Max no. of concurrent processes Default: 1
`-max_array_size`
	Maximum allowed array size to be submitted to the job scheduler
`-pdb_benchmark`	PDB file with the solve structure (for benchmarking)
`-platform`	Platform to execute MR runs (default sge) Default: “sge”
`-environment`	Select a environment for execution of HPC tasks (default None)
`-extend_solution`
	If set, extend partial MR solutions using helical ensembles Default: False
`-queue`	Queue name to send jobs in the HPC (default None)
`-mtz_phases`	MTZ file with phase information (for benchmarking)
`-job_kill_time`	Maximum runtime of each MR run Default: 4320
`-ncontacts_threshold`
	Minimum no. of interhelical contacts to compute CMO of subtarget Default: 35
`-consco_threshold`
	Minimum CMO between predicted and observed contacts to use search model Default: 0.75
`-python_interpreter`
	Indicate a python interpreter for MR runs Default: “/empty/path/bin/ccp4-python”
`-combine_searchmodels`
	If set, combine search models matching different parts of the structure Default: False
`-use_centroids`	Centroids used as search models as well (only if not combining search models) Default: False
`-use_cores`	Core ensembles used as search models as well (only if not combining search models) Default: False