MrParse: an aid to decision making in Molecular Replacement¶
MrParse is a CCP4 program takes a protein amino acid sequence file and searches for homologs using PHMMER (default) or HHSEARCH. If supplied with a reflection data file (currently in MTZ format), it can then use PHASER to calculate the Expected Log Likelihood Gains (eLLG) values for the homologs. It also searches the EBI AlphaFold database for related models.
It also attempts to classify the sequence according to its secondary structure, and whether any regions are expected to be Coiled-Coil or Transmembrane.
MrParse is distributed with CCP4, although optional software can be installed to get the most out of MrParse. Full details are provided here
Simple command line¶
mrparse --seqin <PATH TO SEQUENCE FILE>
To provide a reflection file and classify the sequence we can provide the following optional flags:
--hklin <PATH TO MTZ FILE> --do_classify