Table of Contents
What can PyMOL be used for?
PyMOL is a cross-platform molecular graphic tool and has been widely used for 3D visualization of macromolecules. The utilities of PyMOL have been extensively enhanced by various plugins, including macromolecular analysis, homology modeling, protein–ligand docking, pharmacophore modeling, VS, and MD simulations.
How do I use PyMOL?
The PyMOL Interface
- When PyMOL is opened, two windows appear.
- The lower-right corner of the Viewer contains a guide to using the mouse, as well as a powerful selection tool.
- To run any text command, type it in at a PyMOL> command line and hit [Enter].
Why is PyMOL good?
PyMOL is a great program for looking at molecular structures and making publication quality pictures or movies. You can download an evaluation copy from the DeLano Scientific website which is very easy to install on a windows based machine. There are a number of different mouse modes that can be used in PyMOL.
What is PyMOL in bioinformatics?
PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
Is PyMOL free?
The Software Center has made PyMOL software available for free to all CWRU students, faculty and staff on Windows, Macintosh and Linux machines. PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures.
How can you tell N C or terminus PyMOL?
If you’re looking at a protein molecule in a graphics programme like pymol, then the amino acid with the lowest residue number is the “visible” N-terminus and the one with the highest residue number is the “visible” C-terminus.
What files can PyMOL read?
Supported molecular file formats include: pdb, mol, mol2, sdf, xyz, and others. Supported map formats include: xplor, ccp4, phi, and others. All supported file formats are covered in the reference documentation under File Formats.
Which is better PyMOL or chimera?
Chimera is easier to use than PyMOL to do sophisticated structure analyses, so it would be more appropriate for an advanced course protein structure analysis.
What is better than PyMOL?
Does PyMOL use Python?
General Scripts. General PyMOL scripting is done in Python. It’s really quite simple, just write your function (following a couple simple rules) and then let PyMOL know about it by using the cmd.
What language does PyMOL use?
Python
PyMol is written in Python (hence the name) an extendible scripting language. This language is also popular with the group that develops PHENIX and CCTBX. This means that PyMol can access the powerful scripting features of Python (i.e. you can use Python syntax within PyMol).
How much does PyMOL cost?
Academic and Non-Profit Price List
| PyMOL | ||
| 1 Year Subscription | 3 Year Subscription | |
|---|---|---|
| Professional License for one person | $99 Select >> | $249 Select >> |
| Laboratory & Classroom License for one researcher/instructor and his/her students | $269 Select >> | $689 Select >> |
| Department License for one department | Contact us | Contact us |
Where can I find the documentation for PyMOL?
PyMOL has an extensive help system, and documentation can be found by typing help command for many commands. Measurement of bond distances and angles is straightforward in PyMOL. Structures can be analyzed in a semi-automated way with scripting support.
What can you do with a mouse in PyMOL?
Almost everything you can do with the mouse in PyMOL can also be done by typing commands, and this is one of two places where they can be en- tered. Next, the upper right-hand side of the screen houses the Object Menu Panel, which is used to show/hide objects and selections as well as change many of their properties.
What kind of graphics can you make with PyMOL?
PyMOL can produce high-quality graphics, on par with Molscript, without needing to manually edit text files. PyMOL has an extensive help system, and documentation can be found by typing help command for many commands.
Is the PyMOL project an open source project?
PyMOL 2.5! For previous versions, see here. PyMOL is a commercial product, but we make most of its source code freely available under a permissive license. The open source project is maintained by Schrödinger and ultimately funded by everyone who purchases a PyMOL license.