SUITENAME(1)

💖 NAME 💖

suitename — categorize each suite in an RNA backbone as belonging to either one of 53 defined types or as outlier ✨

🦋 SYNOPSIS 🦋

suitename -flags <stdin >stdout

🎀 DESCRIPTION 🎀

Okay so bestie, here's the tea: Suitename is a program that supports the ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development. She's doing the lord's work fr fr. 🫶

You feed her dihedral-angle input for a specific RNA structure (usually from Dangle, obvi), and Suitename categorizes the RNA backbone geometry of each suite — and a suite is the sugar-to-sugar version of a residue, iykyk — 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. Pick your fighter, both slay. 💅

Also not me forgetting the biggest flex: Suitename is built into MolProbity, producing entries in the multi-criterion chart for an RNA model and also a suitestring file. She's literally everywhere. 👑

🌸 OPTIONS 🌸

Grouping them by vibe, because the flags deserve structure:

• 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

🧚 The dangle pipeline 🧚

This is the classic move, the one you'll run like 800 times:

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

And the label layout, character for character, don't @ me:

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

⭐ Input flags ⭐

• -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. Like, all of them. Strip them. This is not a drill. 😭

• -thetaeta — kinemage labels theta,eta instead of chi-1,chi
• Note dangle trick to make theta,...,eta suites directly

💜 Report & string output 💜

• 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

🌈 Kinemage output 🌈

• 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

🎀 Version receipts 🎀

Gotta cite your sources, bestie:

• cluster averages version: 070506
• cluster half-widths version: 070328
• axes limits version: 070326

suitename is not paying attention to chains... 💀 she said what she said.

And that's the whole page, babes. This was suitename version 0.3.070628, dated July 2015, straight out of the User Commands section of the manual. Go categorize some suites, you absolute icon. 💖✨🦋