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BASIC PYMOL TUTORIAL SOFTWARE
BASIC PYMOL TUTORIAL LICENSE
BASIC PYMOL TUTORIAL DOWNLOAD
BASIC PYMOL TUTORIAL WINDOWS

Below the mouse matrix in the right-hand panel, the word "selecting" is displayed, followed by the selection mode. Single-clicking anywhere on the molecule will make a selection. Right- or double-clicking anywhere in the display pane brings up a viewing menu with a simplified set of options, including a zoom function that automatically fits the molecule to the display size. The editing and viewing modes can be toggled by clicking anywhere in the mouse matrix display. Move clipping plane (cuts off/shadows distant atoms) The important viewing functions are summarized below. The mouse matrix has two main modes, viewing and editing viewing is by far the more useful for our purposes. PyMOL calls its manipulation interface the mouse matrix, which is displayed for reference at the bottom of the right-hand panel in the Viewer window. Manipulating the structure in the Viewer window is easiest with a three-button mouse, as the middle button is assigned unique functions on some systems clicking the right and left buttons simultaneously will simulate a middle-click. When the file is open, the molecule will be displayed in the Viewer window, although not in a particularly attractive representation. Alternatively, you can type load in the Tcl/Tk window, where "filename" is the complete path to the file. You can open the file in PyMOL by clicking File > Open in the window labeled Tcl/Tk GUI and navigating to the location where you saved the file.

BASIC PYMOL TUTORIAL DOWNLOAD

Once you have found the structure you're looking for, click the 'download files' link on the left side of the page, then click the first link labeled "PDB file" and download it to an appropriate location on your computer. The usual place to download a molecular structure file is the PDB website, which allows you to search based on a four-character PDB ID or based on keyword descriptions of a particular structure. The vast majority of published molecular structures will be distributed in this format, which is a human-readable text-based format that you can open and read in any text editor, such as Microsoft Notepad. The standard file format for storing molecular coordinates in the PDB is called a pdb file and usually has the file extension. It contains diagnostic information, error messages, and status output messages that result from commands entered in the Tcl/Tk window.ĭownloading and opening a PDB file īiomolecular structures are deposited in a public database called the Protein Data Bank (PDB).

PyMOL Console: This window is optional, and not launched by default.

navigation bar, as well as a command line and controls for manipulating multi-frame structures (these will generally not be important for our purposes)

PyMOL Tcl/TK GUI: This window contains the familiar File/Edit/etc.

This OpenGL window contains a central area in which the molecule is displayed, a right-aligned column containing information about different selections and representations of the molecule, and a single line labeled PyMOL> at the bottom which functions as a simple command line.

PyMOL Viewer: the window in which molecules are manipulated and displayed.

The PyMOL user interface consists of three components: You will be asked to consider sponsoring the project.Ī number of external plugins and scripts have been developed for PyMol many of these are collected and documented in the PyMol Wiki.īasic usage PyMOL interface overview

BASIC PYMOL TUTORIAL LICENSE

PyMol is copyrighted free software, so please pay attention to the license terms offered to you upon installation. Be sure that you download the build appropriate for your operating system, and follow the appropriate instructions from the PyMOL download site.

BASIC PYMOL TUTORIAL WINDOWS

Precompiled versions of 0.99r6 are available for Windows 2000 or XP, OS X, Linux, IRIX, and Solaris.

We do not intend to support compiling your own version, although it is not difficult. The most current version of PyMol freely available as a precompiled build is 0.99r6, which was released in March 2006 later versions are freely distributed only as source code, and require subscription for access to precompiled versions. Please see the PyMOL download site for complete information.

BASIC PYMOL TUTORIAL SOFTWARE

It is copyrighted free software written and distributed by DeLano Scientific. The official PyMol website is located at Sourceforge.

4.3 Reconstructing biological molecules.