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README
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Membrane protein orientation using a knowledge-based statistical potential
(c) Tim Nugent 2013
Paper
-----
For full details, see http://www.biomedcentral.com/1471-2105/14/276/
Ansible installation
--------------------
First ensure that ansible is installed on your system, then clone the github
repo
% pip install ansible
% git clone https://github.com/psipred/MemEmbed.git
% cd MemEmbed/ansible_installer
Next edit the the config_vars.yml to reflect where you would like MemEmbed
You can now run ansible as per
% ansible-playbook -i hosts install.yml
You can edit the hosts file to install Memebed on one or more machines.
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 (then optionally, make test).
Examples
--------
For a full list of command line paramaters run with a -h flag.
Orientate alpha-helical target using a genetic algorithm:
bin/memembed examples/3o7qA.pdb
Orientate alpha-helical target using a grid search and 8 threads:
bin/memembed -s 1 -a 8 examples/3o7qA.pdb
Orientate alpha-helical target using a direct search:
bin/memembed -s 2 examples/3o7qA.pdb
Orientate beta-barrel target using a genetic algorithm and 8 threads:
bin/memembed -b -a 8 examples/2iahA.pdb
Orientate alpha-helical target with external N-terminal target using
a genetic algorithm, repeating 5 times and retaining the lowest
energy orientation, and printing standard error statistics:
bin/memembed -s 3 -n out examples/2x2v.pdb
Orientate, pre-positioning using topology, and calculate hydrophobic thickness:
bin/memembed -t 4-26,46,68 -n out -q 1 examples/2x2v.pdb
Calculate helix tilt angles:
bin/memembed -z -t 4,26,46,68 -n out examples/2x2v_EMBED.pdb
Orientate target using a specific potential file (see supplementary
data for cross-validated potential files):
bin/memembed -m examples/2iahA.pot examples/2iahA.pdb
Scripts
-------
Both require Pymol to be installed.
Random rotation and translation:
scripts/pymol_rotate.py examples/3o7qA.pdb examples/3o7qA_rotated.pdb
Generate image:
scripts/pymol_membrane_image.py examples/3o7qA_EMBED.pdb examples/3o7qA_EMBED.png
You can add some Pymol api commands around line 26. Defaults to 2 threads (line 12)
Help
----
Please report bugs and suggestions to:
t.nugent@cs.ucl.ac.uk