PyMOL is a molecular visualization tool widely used by the Rosetta community.
The PyMOL Wiki contains documentation on the program methods and numerous examples. Beginners should start with this tutorial. A simple workshop is part of the PyRosetta tutorials.
If you are building PyMOL from source on Linux (this does not take long and is explained here) then you may need to install the python-dev and glutg3-dev packages and possibly the mesa-common-dev package as well. Some notes on building PyMOL for Python 2.7 on a Python 3 system are included below.
Information on making movies in PyMOL can be found at http://www.pymolwiki.org/index.php/PLoS.
PyMOL is so popular in the community, we developed a Mover to send Rosetta data directly to PyMOL.
In PyMOL, run the PyMOL-RosettaServer.py script, found at
<path to Rosetta main>/source/src/python/PyRosetta/src/PyMOL-RosettaServer.py (the main directory of PyRosetta). This will
start the listener and output information about the connection
established. No further work should be required to view PyMOL_Mover
output from the same computer.
We recommend creating a .pymolrc file in your home folder, and adding the following line:
run <path to Rosetta main>/source/src/python/PyRosetta/src/PyMOL-RosettaServer.py
This way is convenient: the PyMOL-Rosetta link is established each time you start PyMOL.
start_rosetta_server
It's that simple. This method of the Server script automatically connects to the machine's current IP. This IP address can be set manually and the Server script defaultly connects at 127.0.0.1. Make sure that the connection is to an accessible IP and that the PyMOL_Mover is outputting to that IP. To change the IP manually use either command below at a PyMOL command prompt:
start_rosetta_server 187.1.3.37, 9001 \\
or
cmd.start_rosetta_server("187.1.3.37","9001")
Here are the options for observing a Rosetta simulation through JD2, Rosetta's job manager). See below for PyRosetta code.
-show_simulation_in_pymol <argument, default=5.0> -update_pymol_on_energy_changes_only 'Boolean'-update_pymol_on_conformation_changes_only 'Boolean'-keep_pymol_simulation_history, 'Boolean'Application of the mover sends pose coordinate data to PyMOL rendering
an image of the structure. Simply apply the mover to a pose. You can
achieve the same results by using dump_pdb to produce a .pdb of the
pose and load it into PyMOL...but the mover is much faster and avoids
unnecessary file writing.\
\
pymover = PyMOL_Mover() pymover.apply(pose)
Use the send_energy method to color the structure in PyMOL based on the residue relative energies. Currently, the color spectrum spans from blue (low energy=happy) to red (high energy=sad). Make sure the pose has been scored first. The send_energy can accept a ScoreType name and color residues in PyMOL based on this score term of the last score function applied.
pymover.send_energy(pose) pymover.send_energy(pose,"fa_atr") pymover.update_energy=True pymover.apply(pose) pymover.energy_type="fa_sol" pymover.apply(pose)
The PyMOL_Mover features a update_energy option which, when True, automatically colors residues by energy when the Mover is applied. The score term sent can be set with the PyMOL_Mover.energy_type option.
To send PyMOL_Mover output to a new IP address, simply change the PyMOL_Mover options as specified below:
pymover.link.udp_ip = '127.0.0.1' pymover.link.udp_port = 65000 pymover.apply(pose)
Another useful PyMOL_Mover feature is the keep_history flag. When marked True, poses with the same "name" (see below) are loaded into new states of the associated PyMOL object ie. applying the PyMOL_Mover does not overwrite the structure in PyMOL but instead loads it into the next state. Protocol movies can be created easily using PyMOL's movie building features and these output states.
pymover.keep_history=True pymover.apply(pose) other_mover.apply(pose) pymover.apply(pose)
To accurately view intermediate changes, you can change the pose name.
This will result in a different object when the pose data is loaded into
PyMOL. To change a pose name use: pose.pdb_info().name("new_name")
Remember, color in PyMOL is per object NOT per state so any successive
coloring will erase the old coloring (another reason you may want to
change the pose name when inspecting a protocol).
The PyMOL_Observer object waits for "events" to happen on the pose and when triggered, applies its own PyMOL_Mover to the structure. This is ideal for situations where you don't want to apply the mover directly, such as lengthy protocols or quick inspection. Since a PyMOL_Observer has a PyMOL_Mover, all the options above can be set on its mover (called pymol) including keep_history, link.udp_ip, and update_energy.
pyobs = PyMOL_Observer() pyobs.add_observer(pose) pyobs.pymol().update_energy=True
Some Linux systems, including Arch based linux such as Manjaro, Antergos and ArchBang, now ship with Python3 as the default. Python2 is also available. Pymol (installed with Python3) does not work with Rosetta's PyMOLObserver.
For compiling and installing Pymol with Python2.7, for a version compatible with Rosetta:
1) Requirements Libraries as well as development files (headers) of the following software is required:
2) Get latest source from SVN Let's say we will download the Pymol source code to /tmp. This will download the latest source to /tmp/pymol:
cd /tmp
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
cd pymolThis will install PyMOL as normal user into ${HOME}/pymol-svn:
prefix=${HOME}/pymol-svn
modules=$prefix/modules
python2.7 setup.py build install --home=$prefix --install-lib=$modules --install-scripts=$prefix${HOME}/pymol-svn/pymolsudo ln -s ${HOME}/pymol-svn/pymol /usr/bin/pymolSo long as you are using this freshly-built pymol, it will work with Rosetta normally; do not use a previously-installed Python3 PyMOL by mistake.