suitename1

Usage

Overview

Suitename is a program that supports the ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development.

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.

Options

output flags: [ -report || -string || -kinemage ]

default: -report -residuein

input flags: [ -residuein || -suitein ]

flags: [ -residuein [ -pointIDfields # ] ] default#==6

OR flags: [ -suitein [ -anglefields # ] ] default#==9

defaults: -residuein -pointIDfields 6 as made by dangle

dangle "alpha, beta, gamma, delta, epsilon, zeta" in.pdb >out.dngl

label : model : chain : number : ins : type : alpha : beta : gamma : delta : epsilon : zeta

-suitein presumes point records from a kinemage {pointID} 7 or 9 anglefields {ptID} [chi] deltam epsilon zeta alpha beta gamma delta [chi]

Note that all other kinemage lines must be stripped off.

-thetaeta kinemage labels theta,eta instead of chi-1,chi

Note dangle trick to make theta,...,eta suites directly

flag: -report [ -chart ] suites in order of input, suiteness summary at end

( -chart : NO summary at end, for MolProbity multichart)

flag: -string 3 character per suite string in order of input

20 per line, ptID of n*20th at end of line

flag: -nosequence only suite names, no Base sequence character

flag: -oneline string all one line, no point IDs

flag: -overlap 20 per line: overlap 10 each line, 10 new per line

flag: -kinemage kinemage of clusters grouped by pucker,pucker ...

group {delta,delta},subgroup {gamma},list {cluster name} assigns to designated wannabe clusters, default: wannabe

flag: -nowannabe to not assign them

[ -power #.#] default# 3.00 multi-dimension distance calc

[ -test ] dump cluster centers, halfwidths,... to stderr

cluster averages version: 070506

cluster half-widths version: 070328

axes limits version: 070326

suitename is not paying attention to chains...