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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
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News & Updates
New Plugin	Bondpack is a a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin	MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce	PyMOL can now be visualized in 3D using Nvidia GeForce video cards (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
New Plugin	GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS.
New Software	CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
New Script	cgo_arrow draws an arrow between two picked atoms.
Tips & Tricks	Instructions for generating movie PDFs using .mpg movies from PyMOL.
Older News	See Older News.

Did you know...
Matrix Copy Matrix_copy copies the object matrix from one object to another. This command is often used after a protein structure alignment to bring other related objects into the same frame of reference. Usage matrix_copy source_name, target_name Arguments source_name = string: name of object to take matrix from target_name = string: name(s) of object(s) to copy matrix to source_mode = integer: 0: raw coordinates, 1: object TTT matrix, 2: state matrix, 3: camera matrix transformation {default: -1: matrix_mode setting} target_mode = integer: (see source_mode) source_state = integer: object state {default: 1} target_state = integer: object state {default: 1} target_undo = 1/0: ??? {default: 1} Example Here's a practical example. We grab two proteins and their density maps. We then align one to the other and then use matrix_copy to move over the density map: <source lang="python"> fetch two proteins and their maps fetch 1rx1 3dau, async=0 fetch 1rx1 ..→

A Random PyMOL-generated Cover. See Covers.

Usage