1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
|
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
.TH CSB-BFIT "1" "November 2017" "csb-bfit 1.2.5" "User Commands"
.SH NAME
csb-bfit \- models non-rigid displacements in protein ensembles with outlier-tolerant probability distributions
.SH DESCRIPTION
usage: csb\-bfit [\-h] [\-c CHAIN1] [\-d CHAIN2] [\-s {student,k}] [\-a ALIGNMENT]
.IP
[\-o OUTFILE] [\-n NITER] [\-\-em]
pdb1 pdb2
.PP
Python application for robust structure superposition of two structures. bfit
models non\-rigid displacements in protein ensembles with outlier\-tolerant
probability distributions.
.SS "positional arguments:"
.TP
pdb1
full path to the first structure
.TP
pdb2
full path to the second structure
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-c\fR CHAIN1, \fB\-\-chain1\fR CHAIN1
Chain of the first structure (default=A)
.TP
\fB\-d\fR CHAIN2, \fB\-\-chain2\fR CHAIN2
Chain of the second structure (default=A)
.TP
\fB\-s\fR {student,k}, \fB\-\-scalemixture\fR {student,k}
Scale mixture distribution (default=student)
.TP
\fB\-a\fR ALIGNMENT, \fB\-\-alignment\fR ALIGNMENT
Alignment in fasta format defining equivalent
positions Assumes that chain1 is the first sequence of
the alignment and chain2 the second sequence
.TP
\fB\-o\fR OUTFILE, \fB\-\-outfile\fR OUTFILE
file to which the rotated second structure will be
written (default=bfit.pdb)
.TP
\fB\-n\fR NITER, \fB\-\-niter\fR NITER
Number of optimization steps (default=200)
.TP
\fB\-\-em\fR
Use the EM algorithm for optimsation (default=False)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
|
