RNAMasonry

RNA Masonry is a computer program that builds atomic models of RNA molecules using recurrent 3D motifs available in RNA Bricks database (https://iimcb.genesilico.pl/rnabricks). The program exploits hierarchical organization of RNA structures, which are composed of regularly shaped double-stranded helices, and irregularly shaped loop motifs. Algorithms implemented in RNA Masonry merge these motifs to build a model that have the user-provided secondary structure, and
plausible local geometry. The program can also use additional restraints like tertiary contacts or small angle scattering data. Here you can download standalone version of the program. Currently only Linux and Mac OSX operating systems are supported.

INSTALLATION

Download

$ tar -zxvf rnamasonry_09.tgz
$ cd rnamasonry_09
$ ./rnamasonry.sh

sync list of frags with the RNA Bricks2 database

$ ./rnamasonry.sh --sync

select example input file

$ cat examples/tRNA.txt
> 1ehz The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution
GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAGgUCcUGUGuuCGaUCCACAGAAUUCGCACCA
(((((((...(((........)))..(((...........)))......((((.......)))).)))))))....

check rnamasonry input options

$ ./rnamasonry.sh
Usage: rnamasonry.py [options]

Options:
  -h, --help            show this help message and exit
  -i FILENAME, --input_file=FILENAME
                        Input file containing RNA sequence and secondary
                        structure or a PDB/mmCIF file. Examples:
                        examples/tRNA.txt,1EHZ.pdb,1EHZ.cif
  -n 4, --n_threads=4   Number of threads [default: 4]
  --local_db=PATH       Path to the fragment database directory [default:
                        /Users/gchojnowski/xprojects/rnamasonry/local_db]
  --refine              Perform a simple simulated annealing refinement only
                        [default: replica exchange]
  --sync                Sync local list of RNA fragments with RNA Bricks2
                        database (updated once a week)
  --steps=1000          Number of MCMC refinement or replica exchange steps
                        [default: 1000]
  -f, --fast            Use no more that 10 frags for each node [default:
                        100]. For testing purposes only.
  --freeze=SELECTION    Keep all fragment with selected nucleotides frozen
                        [e.g. --freeze=12:25,30:39]
  --start-model=FILENAME
                        Path to a json file with dictionary defining starting
                        nodes configuration [default: none]
  --save-decoys=FLOAT   Save given fraction of lowest-energy replica exchange
                        decoys in PDB format [default: 0.0]
  --rg=FLOAT            Target structure radius of gyration [default: none]
  --reference-model=FILENAME
                        Reference model to calculate plot of rmsd vs energy.
  --saxs-data=FILENAME  Experimental SAXS curve for scoring tentative models.
                        This option requires CRYSOL v2.8.3
  --crysol              Use CRYSOL instead of a local FOXS copy (not available
                        on Mac)NOTE: you must provide CRYSOL by yourself

run simulation (using 4 CPU by default)

$ ./rnamasonry.sh -i examples/tRNA.txt

this will start a replica exchange Monte-Carlo model-building simulation for the example secondary structure. After roughly 30 minutes a final model will be saved in a file "rms_tRNA_txt_1/clust_00001.pdb"