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.