Pymol

29,547 downloadsUpdated: September 23, 2020Shareware

Pymolcas
Pymol Educational
Pymol
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Resort to this molecular visualization system in order to carry out minute analyses of proteins, their density, trajectories, and surfaces in 3D mode

What's new in PyMOL 2.4.1-213:

Looking Glass:
Add mouse interactions
Add “Display > Looking Glass” toggle to hide the LG window
Set line_smooth=off for better performance

PyMOL We have a campus-wide license agreement for PyMOL and AxPyMOL. Access to the license keys are limited to current students, faculty, and staff at Stanford.As a subscribing organization, we have access to the latest version of the software, including beta versions, as. PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures. With PyMOL, heavy emphasis is placed on cartoon aesthetics, and so both hydrogen bonding patterns and backbone geometry are used in the assignment. PyMOL is about getting the job done now, as fast as possible, by whatever means were available. PyMOL succeeds in meeting important needs today, but we view it as merely an initial step in a promising direction. In time, we hope that we and others will follow by creating PyMOL.

Read the full changelog

PyMol is a complex tool designed for scientific professionals that need to know the molecular structure of different substances. The application is very complete, open source, and not suitable for beginners.

PyMOL is a lightweight application designed to provide you with a comprehensive molecular visualizing system. Using its integrated ray tracing graphic technique, it can render 3D molecular structures with smoother surface boundary, enhanced shadow and reflection effects.

The main interface is intuitive and clean, which makes is suitable even for beginners. PyMOL provides support for multiple image formats, including PDB, SDF and electron density maps. The rendered images and movies can be saved in session files, which you can share with others, without worrying that the object layout might be changed.

The application comes with all the necessary tools for creating molecular animations and movies. The camera can be rotated to change the perspective, while the built-in animation tool, called RigiMOL, includes a set of features for generating molecular morphs between different structures.

Customizable frame rate, auto-interpolation, loop and ray-tracing framing, image frame caching, slow motion simulations are other advantages that this application comes with.

The generated PyMOL structures can be exported to VRML (Virtual Reality Markup Language), which enables you to create vector graphics using third party applications or print the model with a 3D printer.

PyMOL can display the molecular data using various image representation methods. You can choose from sequence mode, stereo mode, orthoscopic view, lines that emphasize on bond connectivity and more.

The program features customizable colors, structure labels, adjustable object transparency, output and control size, auto-zooming, text overlaying and customizable mouse controls. The built-in wizards assist you in measuring structures, perform pair fitting, adding labels and more.

Altium jtag over usb driver download for windows 10. With its advanced rendering capabilities and movie generation tools, PyMOL is a must-have tool for displaying complex molecular structures and generating live 3D presentations.

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PyMOL is part of these download collections: Chemistry Managers, Genetics Managers

PyMOL was reviewed by Mihaela Teodorovici

4.0/5

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PyMOL 2.4.1-213

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runs on:: Windows All
file size:: 300 MB
filename:: PyMOL-2.4.1_198-Windows-x86_64.exe
main category:: Science / CAD
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PyMOL is a molecular visualization tool widelyused by the Rosetta community.

The PyMOL Wiki containsdocumentation on the program methods and numerous examples. Beginnersshould startwith this tutorial.A simple workshop is part of thePyRosetta tutorials.

If you are building PyMOL from source on Linux (this does not take longand is explainedhere) then you mayneed to install the python-dev and glutg3-dev packages and possibly themesa-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_Mover

PyMOL is so popular in the community, we developed a Mover to sendRosetta data directly to PyMOL. S3y3cam driver download for windows 10.

PyMOL Side

Setting Up 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 willstart the listener and output information about the connectionestablished. No further work should be required to view PyMOL_Moveroutput 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.

Changing PyMOL Listener IP

start_rosetta_server

It's that simple. This method of the Server script automatically connectsto the machine's current IP. This IP address can be set manually and theServer script defaultly connects at 127.0.0.1. Make sure that theconnection is to an accessible IP and that the PyMOL_Mover isoutputting to that IP. To change the IP manually use either commandbelow at a PyMOL command prompt:

Pymol Educational

start_rosetta_server 187.1.3.37, 9001

cmd.start_rosetta_server('187.1.3.37','9001')

Rosetta Usage

Here are the options for observing a Rosetta simulation through JD2, Rosetta's job manager). See below for PyRosetta code.

Attach PyMOL observer to pose at the beginning of the simulation, and outputs a new PyMOL 'state' every seconds. A value of 0 indicates to not skip any packets from sending! Don't forget to run the PyMOLPyRosettaServer.py script within PyMOL!

default = 'false',
'Only Update the simulation in on energy change. Useful if pymol observer is segfaulting on length changes.

default = 'false'
Only update the simulation in pymol on conformation change.

default = 'false'
Keep history when using show_simulation_in_pymol flag?

PyRosetta Usage

Sending Structures

Application of the mover sends pose coordinate data to PyMOL renderingan image of the structure. Simply apply the mover to a pose. You canachieve the same results by using dump_pdb to produce a .pdb of thepose and load it into PyMOL..but the mover is much faster and avoidsunnecessary file writing. pymover = PyMOL_Mover() pymover.apply(pose)

Sending Energy

Use the send_energy method to color the structure in PyMOL based on theresidue relative energies. Currently, the color spectrum spans from blue(low energy=happy) to red (high energy=sad). Make sure the pose has beenscored first. The send_energy can accept a ScoreType name and colorresidues in PyMOL based on this score term of the last score functionapplied.

Download wireless embedded card model 0504 driver. 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. Thescore term sent can be set with the PyMOL_Mover.energy_type option.

Changing Mover IP

To send PyMOL_Mover output to a new IP address, simply change thePyMOL_Mover options as specified below:

pymover.link.udp_ip = '127.0.0.1' pymover.link.udp_port = 65000 pymover.apply(pose)

Keeping History

Another useful PyMOL_Mover feature is the keep_history flag. Whenmarked True, poses with the same 'name' (see below) are loaded into newstates of the associated PyMOL object ie. applying the PyMOL_Mover doesnot overwrite the structure in PyMOL but instead loads it into the nextstate. Protocol movies can be created easily using PyMOL's moviebuilding 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 intoPyMOL. To change a pose name use: pose.pdb_info().name('new_name')Remember, color in PyMOL is per object NOT per state so any successivecoloring will erase the old coloring (another reason you may want tochange the pose name when inspecting a protocol).

PyMOL Observer

The PyMOL_Observer object waits for 'events' to happen on the pose andwhen triggered, applies its own PyMOL_Mover to the structure. This isideal for situations where you don't want to apply the mover directly,such as lengthy protocols or quick inspection. Since a PyMOL_Observerhas a PyMOL_Mover, all the options above can be set on its mover(called pymol) including keep_history, link.udp_ip, andupdate_energy.

pyobs = PyMOL_Observer() pyobs.add_observer(pose) pyobs.pymol().update_energy=True

Getting PyMOLObserver working on a Python3 system

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) RequirementsLibraries as well as development files (headers) of the following software is required:

Subversion
Python (with distutils)
Pmw (Python Megawidgets)
OpenGL driver (NVidia works)
GLEW
GLUT (freeglut)
libpng
freetype
libxml2 (optional, for COLLADA export, disable with --no-libxml)
msgpack-c 1.0+ (optional, for fast MMTF loading, new in SVN r4167, disable with --use-msgpackc=no)

2) Get latest source from SVNLet's say we will download the Pymol source code to /tmp. This will download the latest source to /tmp/pymol:

3) Compiling and installing Pymol

This will install PyMOL as normal user into ${HOME}/pymol-svn:

Now launch PyMOL like this:To add this new PyMOL to your path:4) Connecting to Rosetta

So 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.