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Preparing a new PDB for Rosetta
Jeff Gray has written a series of PDB scripts for manipulation of PDB
files to create Rosetta starting structures. These are located in
$rosetta_scripts/pdb_scripts. The file pdb_scripts.README
in this directory describes how to use these scripts.
- Put the largest docking partner first (Rosetta only moves the
second docking partner in the pdb file; that is, the first partner is
fixed. Put the largest partner first to save CPU time). The
rosetta script extractChains.pl can do this for you--run without
arguments for
usage help.
- Docking partners are separated by a line beginning with 'TER' (as
opposed to the usual pdb format, where TER lines separate different
polypeptide chains). Also put a 'TER' after the last docking
partner. Remove any TER lines between chains of the same docking
partner. Failure to properly place TER lines can cause severe
failure of Rosetta (it can't tell which docking partner is which)
(extractChains.pl can fix the TERs
for you too.)
- If necessary (usually for a blind run), orient the two partners
relative to each other using Swiss PDB
viewer, or another program that you may find more appropriate.
You can do this from scratch, or if you are wish to reproduce the
partner orientation in a related pdb, you can use magic fit to overlay
one of the chains onto its corresponding chain in the "parent" pdb
file. For a blind run, you
will want to put the partners far enough apart that they can rotate
freely relative to each other, but no farther apart than that (this
will tend to cause a lot of contact failures)
- A final (but important) point. The way rosetta is set up,
pdb codes must be exactly four letters long (standard pdb
format). If you give it a pdb code that is either less or more
than four characters, different parts of the code will handle the
illegal pdb code differently, usually resulting in some cryptic file
path error. It is best not to commit this error in the first
place as the resulting problems are hard to decode.
For example, if your two docking partners are chainL+chainH (one
partner) and chain A, and chain L + chain H is larger than chain A,
then you will want to format your pdb as follows:
<chain L>
<chain H>
TER
<chain A>
TER
Note there is no TER between L and H because they are in the same
docking partner.
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