/barnaba

Primary LanguageCGNU General Public License v3.0GPL-3.0

Build Status

INTRODUCTION

BaRNAba is a tool for analyzing RNA three-dimensional structures. BaRNAba has been developed by Sandro Bottaro with the crucial help of Giovanni Bussi. For bugs, questions or comments contact Sandro at sbottaro@sissa.it. If you use baRNAba in your work, please cite the following paper:

S.Bottaro, F. di Palma, G.Bussi. The role of nucleobases in RNA structure and dynamics. Nucleic Acids Research (2014)

INSTALLATION

BaRNAba is distributed as a Python script. It requires Python version 2.7 with Numpy and Scipy libraries.

You can obtain barnaba using git:

git clone git://github.com/srnas/barnaba.git

or download a zip file from the web:

https://github.com/srnas/barnaba

USAGE

  • minimal help ./baRNAba --help

Currently, baRNAba can perform different tasks:

  1. Calculate the ERMSD between structures ./baRNAba ERMSD --pdb sample1.pdb -f sample2.pdb ...

  2. Calculate ESCORE ./baRNAba ESCORE --force-field 1S72.pdb -f sample1.pdb ...

  3. Find hairpin loop motif ./baRNAba SS_MOTIF --query motif.pdb -f file1.pdb file2.pdb ...

  4. Find double stranded motif. l1 and l2 are the lengths of the two strands ./baRNAba DS_MOTIF --query motif.pdb -f file1.pdb file2.pdb ... --l1 l1 --l2 l2

  5. Annotate structures/trajectories according to the Leontis/Westhof classification.
    ./baRNAba ANNOTATE -f file1.pdb file2.pdb ...

  6. Calculate dihedral backbone angles ./baRNAba TORSION -f file1.pdb file2.pdb ... --backbone --hread

  7. Calculate dihedral pucker angles ./baRNAba TORSION -f file1.pdb file2.pdb ... --pucker --hread

  8. Calculate J-couplings (H1'H2', H2'H3' H3'H4', H4'H5', H4'H5'',1H5P,2H5P,H3P_+) ./baRNAba TORSION -f file1.pdb file2.pdb ... --jcoupling --hread

  9. Calculate NOE signal ./baRNAba NOE -f file1.pdb file2.pdb

GROMACS XTC FILES

baRNAba can read xtc trajectory files as well if the library libxdrfile2 is correctly installed:

cd xtc
python setup.py build --build-lib=.
python setup.py install --user

xtc files can be read using the --xtc argument. The topology file, in PDB format, has to be specified using -f, for example

./baRNAba ERMSD --pdb sample1.pdb -f sample2.pdb --xtc samples.xtc

calculates the ERMSD between sample1 and sample2, and all snapshots in samples.xtc sample2.pdb must contain all the atoms (in the correct order!) as in the xtc file.