Downloading RIBFIND2
RIBFIND2 can be installed directly from PyPI. Simply
run pip install ribfind. RIBFIND2 requires the
DSSP and RNAView programs to be installed.
Running RIBFIND2
The RIBFIND2 command-line interface accepts a model in PDB format and either a DSSP file, and RNAView XML file or both. Parameters such as the contact distance for amino acids, nucleic acids can be set via additional command-line arguments.
Examples
For the following examples, you will need to download:
Example: Running on a RIBFIND to predict rigid bodies from DSSP secondary structure prediction. The output will be in a directory called '1mji'.
$ ribfind --model 1mji.pdb --dssp 1mji.dssp
Example: Running on a RIBFIND to predict rigid bodies from RNAView secondary structure. The output will be in a directory called '1mji'.
$ ribfind --model 1mji.pdb --rnaml 1mji.xml
Example: Running on a RIBFIND to predict rigid bodies from RNAView secondary structure and DSSP output. The output will be in a directory called '1mji'.
$ ribfind --model 1mji.pdb --rnaml 1mji.xml --dssp 1mji.dssp
The full range of command line options can be discovered by typing ribfind --help. The output is shown below as a reference.
ribfind [-h] --model MODEL [--dssp DSSP] [--rnaml RNAML]
[--protein-cutoff-dist PROTEIN_CONTACT_DISTANCE]
[--protein-helix-ratio PROTEIN_HELIX_RATIO]
[--protein-dens-cutoff PROTEIN_DENS_CUTOFF]
[--protein-minimum-strand-length PROTEIN_MINIMUM_STRAND_LENGTH]
[--rna-contact-dist RNA_CONTACT_DISTANCE]
[--rna-minimum-strand-length RNA_MINIMUM_STRAND_LENGTH]
[--rna-dens-cutoff RNA_DENS_CUTOFF]
Output
RIBFIND2 produces rigid-body files which can be used with Flex-EM or TEMPy-REFF.