GARN: Sampling RNA 3D structure space

GARN2 User Manual

GARN2 is a JAVA application
To use GARN, you need JAVA (version 1.7).

GARN2 use Fasta file :

To create a GARN file from a PDB file (from a PDB file):

java -jar ./GARN2.jar PDBTOGARN ‹Name of molecule› ‹Fasta File› ‹Location of the PDB file›
Example: java -jar ./GARN2.jar PDBTOGARN 1E8O 1E8O_fasta.txt 1E8O.pdb
Output two files : ‹Name of molecule›_GARN.csv with the position of nodes in 3D space, and ‹Name of molecule›_listNucleo.csv, to indicate the correspondance between nodes and nucleotides.

To compute the sampling space:

java -jar ./GARN2.jar GAME ‹Name of molecule› ‹Fasta File› ‹Number of solutions›
Example: java -jar ./GARN2.jar GAME 1E8O 1E8O_fasta.txt 10
Output 10 files : GARN_‹Name of molecule›_0.csv, & GARN_‹Name of molecule›_1.csv

To compute the sampling space and compute RMSD:

java -jar ./GARN2.jar GAME ‹Name of molecule› ‹Fasta File› ‹Number of solutions› ‹GARN file of native structure›
Example: java -jar ./GARN2.jar GAME 1E8O 1E8O_fasta.txt 10 1E8O_GARN.csv
Output 11 files : GARN_‹Name of molecule›_0.csv, & GARN_‹Name of molecule›_1.csv, ... and a ‹Name of molecule›_out.csv with the RMSD and the Maximum distance (to sort the sampling).

To compute the RMSD between GARN files (compare to one file):

java -jar ./GARN2.jar RMSD ‹Name of molecule› ‹GARN file of molecule to compare› ‹GARN file of molecule 2›....
Example: java -jar ./GARN2.jar RMSD 1E8O 1E8O_GARN.csv GARN_1E8O_1.csv GARN_1E8O_2.csv GARN_1E8O_3.csv GARN_1E8O_4.csv
Output 1 files : ‹Name of molecule›_rmsd.csv with the RMSD between the first file and others files.

To compute the maximum distance in structure and sort the sampling:

java -jar ./GARN.jar SORT ‹Name of molecule› ‹GARN file of molecule 1› ‹GARN file of molecule 2› ...
Example: java -jar ./GARN2.jar SORT GARN_1E8O_1.csv GARN_1E8O_2.csv GARN_1E8O_3.csv GARN_1E8O_4.csv
Output 1 files : ‹‹Name of molecule››_sort.csv with the maximum distance for each solution.

Possible errors: