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README
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Modification of FILM3 algorithm to incorporate membrane potential term
(c) Tim Nugent 2013
Paper
-----
For full details, see:
http://www.pnas.org/content/early/2012/05/21/1120036109
http://www.biomedcentral.com/1471-2105/14/276/
Compiling
---------
Tested under Ubuntu 13.04 and CentOS 5.4.
Requires Boost headers and libraries - specifically boost_thread and boost_system. On recent Debian/Ubuntu distributions, install these packages:
libboost-thread1.49-dev
libboost-thread1.49.0
libboost-system1.49-dev
libboost-system1.49.0
or just install them all:
libboost-all-dev
Then to compile, just run make.
Usage
-----
Refinement using contactrecomb:
-------------------------------
./contactrecomb input/2nq2A_ensemble.pdb input/2nq2A.con input/2nq2A.ess input/2nq2A.zcoord 1.6 500 8 output.pdb
This is the protocol that was used in the BMC Bioinformatics paper. The arguments are:
2nq2A_ensemble.pdb : ensemble of candidate structures, generated by superposing candidates on to the FILM3 recombined model
2nq2A.con : contacts predicted by PSICOV
2nq2A.ess : secondary structure
2nq2A.zcoord : z-coordinates
1.6 : membrane potential energy weighting
500 : poolsize for genetic algorithm used to orientate target
8 : threads to use for orientation
output.pdb : output PDB file
Where you see a line like this:
Emin = 1187.153809
A lower energy structure has been found.
Folding using FILM3:
--------------------
./film3 input/1gzmA.nfpar test.pdb
Some new options have been added to the nfpar file:
# Use GA for orientation, otherwise direct search
ORIENTGA 1
# Weighting for membrane potential energy term
ENVWT 0.002
# Threads to use for orientation
THREADS 8
# Maximum GA calls for orientation
MAXGACALLS 10000
# GA poolsize for orientation
GAPOOLSIZE 500
# Skip the original FILM3 Z-coord minimum distance test
SKIPZTEST 1
# Fold helix by helix
FOLDBYHELIX 1
The last option FOLDBYHELIX begins the simulation with just 2 TM helices, and adds helices sequentially throughout the simulation.
You can monitor the simulation using the monitor.py script:
pymol scripts/monitor.py
This will automatically reload the file test.pdb every few seconds.
Help
----
Please report bugs and suggestions to: