MrParse options¶
MrParse Molecular Replacement Search Model analysis
usage: mrparse [-h] [-hkl HKLIN] [--do_classify] [--pdb_dir PDB_DIR]
[--phmmer_dblvl {50,70,90,95,100}] [--run_serial] [-seq SEQIN]
[--search_engine {phmmer,hhsearch}] [--tmhmm_exe TMHMM_EXE]
[--deepcoil_exe DEEPCOIL_EXE] [--hhsearch_exe HHSEARCH_EXE]
[--hhsearch_db HHSEARCH_DB] [--ccp4cloud] [-v]
Named Arguments¶
- -hkl, --hklin
MTZ/CIF Crystal Data file
- --do_classify
Run the SS/TM/CC classifiers - requires internet access.
Default: False
- --pdb_dir
Directory of PDB files
- --phmmer_dblvl
Possible choices: 50, 70, 90, 95, 100
Redundancy level of PDB database used by Phmmer
Default: “95”
- --run_serial
Run on a single processor
Default: False
- -seq, --seqin
Sequence file
- --search_engine
Possible choices: phmmer, hhsearch
Select search engine
Default: “phmmer”
- --tmhmm_exe
Location of TMHMM executable for transmembrane classification
- --deepcoil_exe
Location of Deepcoil executable for coiled-coil classification
- --hhsearch_exe
Location of hhsearch executable
- --hhsearch_db
Location of hhsearch database
- --ccp4cloud
specify running through CCP4Cloud
Default: False
- -v, --version
show program’s version number and exit