Useful scripts coming with forgi¶

Forgi comes with a few scripts in the example folder. The most useful ones get installed automatically and are explained here.

Visualization script¶

The script visualize_rna.py is a wrapper around PyMol for visualizing PDB structures and coarse-grain RNA structures in the forgi file format. This script created a coarse grained representation of the RNA based on structural elements as compiled graphics object and displays it along the all-atom structure (if present).

To view a pdb file use:

visualize_rna.py 1jj2.pdb

This will display a cleaned version of the original PDB structure (with proteins removed) together with the secondary structure representation as compiled graphics object. In addition, selections for each stem and loop element are defined. You can use PyMol’s “Load” button to load the raw PDB (with proteins) into PyMol. It will be oriented correctly.

If you view a file in the forgi file format (visualize_rna.py 1y26.cg), only the compiled graphics object will be shown, because no all-atom coordinates are present.

Use visualize_rna.py -x 1y26.cg to show coarse-grained element names.

Use visualize_rna.py --virtual-atoms 1y26.cg to show virtual atoms for the backbone and visualize_cg.py --sidechain-atoms 1y26.cg to show all virtual atoms. Virtual atoms are not the true atom positions, but instead calculated based on ideal helices, the coarse-grained helix twist and the coarse-grained helix coordinates.

File format conversions¶

To convert files between the file formats “fasta with secondary structure”, “dotbracket string”, “coarse-grain forgi file”, “bpseq”, “pdb”, “mmcif” and “ct”, use the rnaConvert.py script:

rnaConvert.py 1jj2.pdb -T forgi

The -T option specifies the output file format.

Use -T forgi to create a “.bg” or “.cg” file, -T fasta for a fasta-file with secondary structure, -T bpseq for a bpseq-file and -T dotbracket to only output a dotbracket string.

You can use the --to-file or the --filename OUTNAME option to write to files instead of STDOUT.

If --to-file is used, files with the RNA’s name will be created in the current directory. In the case of PDB files as input, the RNA’s name is the PDB-id followed by an underscore and the chain ids separated by a dash. For fasta-files, the name is given in the first line after the ‘>’-symbol. If no name is given, “untitled” is used.

The --filename option can be used to specify an alternative file- or directory-name. Note that the file extension will be appended automatically. If the input-file contains multiple RNA molecules (connected components), a file will be created for each of them, with numbers appended to the filename.

Render the graph-representation of a Bulge Graph as an image¶

Run the following command, which requires neato (http://www.graphviz.org/), to generate an svg image of the graph represenation of the RNA:

rnaConvert.py 1y26.cg -T neato | neato --Tsvg -o /tmp/test.svg

Get a representation of the coarse grain element names that correspond to dots and brackets¶

Use:

rnaConvert.py 1y26_ss.dotbracket -T element_string

This will print:

(((((((((...(((((((.......)))))))........((((((.......))))))..)))))))))
sssssssssmmmssssssshhhhhhhsssssssmmmmmmmmsssssshhhhhhhssssssmmsssssssss
00000000000011111110000000111111122222222222222111111122222211000000000

The numbers indicate the numbers of the coarse grained elements. As expected, the first column holds the values ‘(‘,’s’,‘0’ indicating that this opening bracket belongs to the stem “s0”. This is especially useful when writing tests for the forgi library or code depending on it.

Update cg-files created with earlier versions of forgi¶

If you use CoarseGrainRNA files (*.cg/ *.coord files) that were created before release of version 1.0, you might get an AssertionError saying that the twists are inconsistent. Due to a bug in earlier versions of forgi, some twist vectors could sometimes deviate by a few degrees from being orthogonal to the stem vector. To use such broken *.cg files with newer versions of forgi, you can use the example script: fix_twists.py

A list of all scripts¶

all_atom_positions.py and average_atom_positions.py were used to generate the file forgi/threedee/data/average_atom_positions.json, which comes with forgi.
burial.py: Characterize a pdb file.
compare_RNA.py: Calculate RMSD and ACC between 2 3D structures.
projection_rmsd: Calculate the 2D RMSD between two 2D projections of Coarse Grained RNA objects.
coaxial_stacking.py: Experimental.

forgi 2.0.0 documentation