RCrane.CLI takes input of a PDB file containing phosphates, bases, and C1' atoms, and uses these coordinates to predict and build backbone conformers. This is done using the methodology described in:

Keating KS and Pyle AM. Semiautomated model building for RNA crystallography using a directed rotameric approach. Proc Natl Acad Sci USA, 107: 8177-8182 (2010).

Note that all publications resulting from use of this program must acknowledge this manuscript.

Please also note that RCrane.CLI is a command line program and is not intended for interactive use. Crystallographers wishing to use this methodology for structure building should use RCrane, which is a Coot plugin that allows for faster and easier building of RNA into electron density. RCrane is available from http://pylelab.org/software/.

RCrane.CLI is copyright 2010, Kevin Keating, and is licensed under the Educational Community License, Version 2.0.

INSTALLATION INSTRUCTIONS

RCrane.CLI requires Perl 5, version 5.8 or newer. If you are using Linux or Macintosh OS X, Perl should already be installed on your computer. If you are using Windows, you may install ActivePerl (http://www.activestate.com/activeperl/) or Strawberry Perl (http://strawberryperl.com/).

RCrane.CLI also requires the Math::Interpolate and Math::Amoeba Perl modules. If using Perl on Linux or OS X these modules may be installed from:

http://search.cpan.org/~bzajac/Math-Interpolate-1.05/lib/Math/Interpolate.pm
http://search.cpan.org/~tom/Math-Amoeba-0.05/lib/Math/Amoeba.pm

If using ActivePerl, these modules may be installed using the Perl Package Manager included with ActivePerl. If using Strawberry Perl, these modules may be installed using the interactive CPAN shell.

Once Perl and the necessary modules are installed, RCrane.CLI may be installed by simply unzipping the program into any desired directory (ex. /usr/local/xtal/rcrane.cli/ or C:\Program Files\RCrane.CLI\). Users may wish to place this directory in their path (or create a symbolic link in the appropriate directory).

RUNNING RCRANE.CLI

RCrane.CLI must be run from the command line. Input for RCrane.CLI is a PDB file containing phosphates, bases, and C1' atoms. (Note that RCrane.CLI does not help with the placement of these atoms. The Coot plugin will help a crystallographer in placing these atoms and will be released in summer 2010.) If RCrane.CLI is installed in one of the locations described above and the necessary atoms are placed in struc.pdb, the program may be invoked as follows:

/usr/local/xtal/rcrane.cli/rcrane.cli.pl struc.pdb
     or
"C:\Program Files\RCrane.CLI\rcrane.cli.pl" struc.pdb

After the program has finished running, four output files will be generated:

struc.built.pdb

A PDB file containing a molecule constructed using the most likely conformers

struc.data.csv

A table containing all data used for the conformers predictions: theta', eta', base-phosphate perpendicular distances, C1'-C1' distances, and P-P distances

struc.probs.csv

A table containing the probabilities for each conformer at each suite of the structure

struc.rots.csv

A table containing the three most likely conformers for each suite, along with their sugar puckers. The bottom of this table also contains a conformer string for the most likely conformers.

Additional options are described in MANUAL.txt or by running rcrane.cli.pl -m.

CHANGELOG

version 1.0.1
Changed name from CONDOR.CLI to RCrane.CLI
Updated PNAS citation

version 1.0
Initial release