The scripts and input files that accompany this demo can be found in the
demos/public directory of the Rosetta weekly releases.
KEYWORDS: MEMBRANES ANALYSIS
Author: Julia Koehler Leman (julia dot koehler1982 at gmail dot com)
Corresponding PI: Jeffrey J. Gray (jgray at jhu dot edu)
Last Updated: 12/18/2014
Rosetta Revision #58069
This script generates a spanfile from a PDB file. A span file is a topology file read into Rosetta and is generally generated from a membrane proteins sequence using the OCTOPUS server (http://octopus.cbr.su.se/) which is then converted into a spanfile using octopus2span.pl. This app generates a spanfile from a PDB file for easy testing of membrane applications, when the structure is known.
Generate a PDB file where the membrane protein structure (our case 1AFO) is transformed into PDB coordinates (z-axis is membrane normal). This can be done either by downloading the transformed PDB directly from the PDBTM website (http://pdbtm.enzim.hu/) or by downloading a PDB file from the PDB and running it through the PPM server (http://opm.phar.umich.edu/server.php). If you don't have it, you can copy the provided file:
$> cp input/1AFO_tr.pdb .
Clean the PDB file by using clean_pdb.py in the folder Rosetta/tools/protein_tools/scripts/:
$> $ROSETTA_TOOLS/protein_tools/scripts/clean_pdb.py 1AFO_tr.pdb ignorechain
An example input is provided in the input folder: 1AFO_AB.pdb (your file will be named 1AFO_tr_ignorechain.pdb that you can rename).
Run the command.sh script provided in this folder: (where
$> $ROSETTA3/bin/spanfile_from_pdb.default.linuxclangrelease -in:file:s input/1AFO_AB.pdb
This generates three spanfiles in the input (! unfortunately) folder. For this demo, these files have been moved into the output folder.
1AFO_AB.span spanfile of full PDB 1AFO_ABA.span spanfile of chain A 1AFO_ABB.span spanfile of chain B in isolation (i.e. residue numbering starts from 1)
Please check the span file for errors and report errors to julia dot koehler1982 at gmail dot com!