RCrane.CLI (formerly CONDOR.CLI)
Author: Kevin Keating
Description: RCrane.CLI uses phosphate and glycosidic bond coordinates to predict and build backbone structure. 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, above.
Reference: Keating KS and Pyle AM. Semiautomated model building for RNA crystallography using a directed rotameric approach. Proc Natl Acad Sci USA, 107 (2010) 8177-8182.
Downloading and installation instructions: Please click here to download RCrane.CLI. Instructions for installing and running the program may be found here.
Description: AMIGOS reads an RNA PDB file and outputs a complete table of torsion angle calculations. more info.
Current version: 0.3 (2003-Aug-30)
Downloading and installation instructions: AMIGOS is a Perl script - it does not need compilation. Just download the script from the link below, check to ensure Perl is properly installed on your machine, and make the file AMIGOS executable. The program is ready to use. The output of the program is a series of spreadsheets containing conformational data. If you use KaleidaGraph to view spreadsheet data, the plot template from the figure above will assist you in viewing the data.
AMIGOS.pl: AMIGOS 0.3
README.txt: README file
template_all.hqx: binhexed Mac KaleidaGraph plot template
amigos.tar.gz: all the above in one tarred and gzipped archive.
Description: PRIMOS allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures. Note that the search capabilities of PRIMOS are also included in AMIGOS II.
Downloading and installation instructions: Please contact us if you would like to use PRIMOS. You will be required to sign a license agreement, and then we will provide the software and installation instructions by email. It is free for academic use but carries a charge for industrial use.