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.

Reference:

  • Alford RF, Koehler Leman J, Weitzner BD, Duran A, Elazar A, Tilley D, Gray JJ (2015): An integrated framework advancing membrane protein modeling and design, PLosONE (in preparation)

Executable/Script

main/source/bin/spanfile_from_pdb.macosclangrelease

Generating Inputs

  1. 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 .

  2. 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

  3. 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).

Running the Application

Run the command.sh script provided in this folder: (where $ROSETTA3=path-to-Rosetta/main/source)

$> $ROSETTA3/bin/spanfile_from_pdb.default.linuxclangrelease -in:file:s input/1AFO_AB.pdb

Example Outputs

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!