I am wondering about the alignment of sequence and PDB model in mr_rosetta - the program seems to complain if the sequences dont

exactyl match - so is this really the case? (I have an initial model from autobuild with some fragments that do not have fully correct sequence - hence

it doenst exactly match with the original sequence of the protein). Does it have to? Or should there be a way around it?

also the command file examples online e.g. :

phenix.mr_rosetta \
  seq_file=seq.dat \
  data=coords1.mtz \
  search_models=coords1.pdb \
  already_placed=True \
  rescore_mr.relax=False \
  rosetta_models=20 \
  ncs_copies=2 \
  space_group=p212121  \
  use_all_plausible_sg=False \
  nproc=200 \
  group_run_command=qsub

when using the command file all the commands are not recognized for some reason (running on a mac with bash shell) e.g. 

rescore_mr.relax=False, same with fragment files… not quite sure what the problems is there, probably something trivial.

-if i just enter them on the command line it works.

Thanks,