.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
.TH SUITENAME "1" "July 2015" "suitename 0.3.070628" "User Commands"
.SH NAME
suitename \- categorize each suite in an RNA backbone as belonging to either one of 53 defined types or as outlier
.SH SYNOPSIS
.B suitename
\fB\-flags\fR <stdin >stdout
.SH DESCRIPTION
.P
Suitename is a program that supports the ROC RNA Ontology Consortium
consensus RNA backbone nomenclature and conformer-list development.
.P
From dihedral-angle input for a specific RNA structure (usually from
Dangle), Suitename categorizes the RNA backbone geometry of each suite
(the sugar-to-sugar version of a residue) either as an outlier ("!!") or
as belonging to one of the 53 defined conformer bins. The output is
either a one-line-per-suite report, or a linear conformer string (as
shown below the image here) in one of several variant formats. Suitename
is built into MolProbity, producing entries in the multi-criterion chart
for an RNA model and also a suitestring file.
.SH OPTIONS
.IP
output flags: [ \fB\-report\fR || \fB\-string\fR || \fB\-kinemage\fR ]
.IP
default:  \fB\-report\fR \fB\-residuein\fR
.IP
input flags: [ \fB\-residuein\fR || \fB\-suitein\fR  ]
.IP
flags: [ \fB\-residuein\fR [ \fB\-pointIDfields\fR # ] ] default#==6
.IP
OR flags: [ \fB\-suitein\fR [ \fB\-anglefields\fR # ] ] default#==9
.IP
defaults: \fB\-residuein\fR  \fB\-pointIDfields\fR 6
as made by dangle
.IP
dangle "alpha, beta, gamma, delta, epsilon, zeta" in.pdb >out.dngl
.IP
label : model : chain : number : ins : type : alpha : beta : gamma : delta : epsilon : zeta
.IP
\fB\-suitein\fR presumes point records from a kinemage
{pointID} 7 or 9 anglefields
{ptID} [chi] deltam epsilon zeta alpha beta gamma delta [chi]
.PP
Note that all other kinemage lines must be stripped off.
.IP
\fB\-thetaeta\fR  kinemage labels theta,eta instead of chi\-1,chi
.PP
Note dangle trick to make theta,...,eta suites directly
.IP
flag: \fB\-report\fR [ \fB\-chart\fR ]
suites in order of input, suiteness summary at end
.IP
( \fB\-chart\fR : NO summary at end, for MolProbity multichart)
.IP
flag: \fB\-string\fR
3 character per suite string in order of input
.IP
20 per line, ptID of n*20th at end of line
.IP
flag: \fB\-nosequence\fR
only suite names, no Base sequence character
.IP
flag: \fB\-oneline\fR
string all one line, no point IDs
.IP
flag: \fB\-overlap\fR
20 per line: overlap 10 each line, 10 new per line
.IP
flag: \fB\-kinemage\fR
kinemage of clusters grouped by pucker,pucker ...
.IP
group {delta,delta},subgroup {gamma},list {cluster name}
assigns to designated wannabe clusters, default: wannabe
.IP
flag: \fB\-nowannabe\fR   to not assign them
.IP
[ \fB\-power\fR #.#] default# 3.00 multi\-dimension distance calc
.IP
[ \fB\-test\fR ] dump cluster centers, halfwidths,... to stderr
.PP
cluster averages version: 070506
.PP
cluster half\-widths version: 070328
.PP
axes limits version: 070326
.PP
suitename is not paying attention to chains...