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QUEEN stands for: "QUantitative Evaluation of Experimental Nmr restraints"

QUEEN objectively sorts distance and dihedral angle restraints by "importance" without ever calculating 3D structures.

Usually only ~10% of restraints contain most information about the structure - therefore these restraints have to be correct for good structure calculations.

Project home page is here



The QUEEN program estimates information content in each restraint by calculating how much a given restraint improves uncertainty in the distance geometry matrix (DG matrix). DG matrix is calculated by NIH-XPLOR which is called internally from the QUEEN package.

Knowing which restraints are more important allows to save a lot of time spent on checking correctness of restraint assignments (since it is known that e.g. typically only ~10% of NOE restraints provide most information for the structure calculations).

Limitations: (1) program only works with proteins; does not work for DNA, RNA or other molecules; (2) only 32-bit linux version available

Running time: depends on number of restraints in the table and size of polypeptide, typically takes from half hour to 1 day on a relatively fast desktop computer.

Requirements: python, NIH-XPLOR, 32-bit Linux OS

Quick guide

Preparing input

  • go to directory where queen is installed
  • come up with a name for your project
  • type
./generate.py --project <projectname>
  • this will create the necessary directory structure
  • collect restraint files in your project directory
  • check restraint files (restraint files must have .tbl extensions and must be in XPLOR format)
./restraints.py --check distance-restraints.tbl -o good-distance-restraints.tbl
./restraints.py --check -d dihedral-restraints.tbl -o good-dihedral-restraints.tbl
  • the good ones will be saved into the files specified with -o flag
  • copy good restraints to <projectname>/data/restraints directory
  • set up data set file <setname.list> (extension is important), place file into <projectname>/data/datasets
  • almost done. Now you'll need sequence, .psf and .pdb files. You have two choices

Starting with a sample pdb file (easier setup)

  • type
./generate.py --pdb2all <projectname> sample.pdb 
  • this will create the psf and protein sequence files

No pdb file (harder setup)

  • prepare a sequence file in three letter format (explained below)
  • if you have one-letter sequence file with a single chain, this script will do the job
  • type
./generate.py --seq2psf <projectname> <sequence file>
  • this should create psf file
  • now type
./generate.py --psf2tem <projectname> <projectname>/data/sequence/protein.psf
  • this will create template pdb file from the .psf file

Checking input and running the program

  • check the project
queen.py --check <projectname> <setname>
  • run it
queen -Iuni <projectname> <setname>

Sequence file format

>A (these chain names must be present)

Format for dataset files

dataset files must have .list extensions and must be placed into <projectname>/data/datasets directory

NAME = NOE restraints
FILE = good-noe-restraints
NAME = Dihedral angle restraints
FILE = good-dihedral-restraints
INFO = no

INFO field is optional. If "INFO = no" is used, these restraints won't be added to the ranked output


  1. Nabuurs, SB and Spronk, CAEM and Krieger, E and Maassen, H and Vriend, G and Vuister, GW. Quantitative Evaluation of Experimental NMR Restraints. J Biomol NMR 3:55--66, 1993. BibTeX [queen]
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