bionic (1) csb-bfit.1.gz

NAME

       csb-bfit  -  models  non-rigid  displacements  in  protein  ensembles  with  outlier-tolerant probability
       distributions

DESCRIPTION

       usage: csb-bfit [-h] [-c CHAIN1] [-d CHAIN2] [-s {student,k}] [-a ALIGNMENT]

              [-o OUTFILE] [-n NITER] [--em] pdb1 pdb2

       Python  application  for  robust  structure  superposition  of  two  structures.  bfit  models  non-rigid
       displacements in protein ensembles with outlier-tolerant probability distributions.

   positional arguments:
       pdb1   full path to the first structure

       pdb2   full path to the second structure

   optional arguments:
       -h, --help
              show this help message and exit

       -c CHAIN1, --chain1 CHAIN1
              Chain of the first structure (default=A)

       -d CHAIN2, --chain2 CHAIN2
              Chain of the second structure (default=A)

       -s {student,k}, --scalemixture {student,k}
              Scale mixture distribution (default=student)

       -a ALIGNMENT, --alignment ALIGNMENT
              Alignment  in fasta format defining equivalent positions Assumes that chain1 is the first sequence
              of the alignment and chain2 the second sequence

       -o OUTFILE, --outfile OUTFILE
              file to which the rotated second structure will be written (default=bfit.pdb)

       -n NITER, --niter NITER
              Number of optimization steps (default=200)

       --em   Use the EM algorithm for optimsation (default=False)

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.