QUEEN
From NMR Wiki
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
Contents |
Summary
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) ALA GLU PRO ... >B ...
Format for dataset files
dataset files must have .list extensions and must be placed into <projectname>/data/datasets directory
NAME = NOE restraints TYPE = DIST FILE = good-noe-restraints // NAME = Dihedral angle restraints TYPE = DIHE 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
