PyMOL Molecular Viewer

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PyMOL is Good for:

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·  OPEN SOURCE CODE (SVN),
·  FREE EVALUATION BUILDS,
·  INCENTIVE DOWNLOADS*, or
·  OFFICIAL DOCUMENTATION*
* = extra benefits for project sponsors.

PyMOL: Molecular Virtual Reality

Please visit the PyMOL
FREE COMMUNITY WIKI
and
MAILING LIST ARCHIVE!

PyMOL runs on:

Linux & Unix

and

"A link is a vote", so
please link www.pymol.org!

TRACKERS:

PyMOL supporters:

Our founder, Warren DeLano, passed away suddenly on November 3, 2009. We want to reassure the community that DeLano Scientific is still in business, PyMOL is still available for download, customers who have purchased support subscriptions are still receiving support, and we continue in our commitment to the open source community. In addition, we are once again accepting new subscription requests; however, there will likely be delays in processing orders and answering sales emails while we work through the present circumstances.

We ask that you please use the following information to contact DeLano Scientific:

U.S. Mail and faxes may continue to be sent to addresses and fax numbers posted on our website.

All sales related inquiries and business matters should be directed to sales@delsci.com.

For customers who have purchased support subscriptions, please direct support requests to the email address designated for this purpose. If you have purchased a support subscription and are unsure which email address to use, please contact sales@delsci.com.

We ask that you please refrain from sending email to Warren’s personal email address (warren@delsci.com), and from leaving messages in the business voicemail at this time (650-283-6945). If you need to speak to someone live, the best way to do so is to email us and tell us how to contact you.

We have been deeply touched by the response and support we have received from the community, and we ask that you please bear with us while we plan for PyMOL’s future.

Beth Pehrson

PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation. Please support development of this open, effective, and affordable software by purchasing a subscription to maintenance and/or support. Thank you!

Latest News

October 5, 2009: Updated PyMOL 1.2r2 builds have been posted for Mac, Windows, and Linux. This update fixes several annoying bugs present in 1.2r1. Current PyMOL Subscribers may download version 1.2 builds directly or access them through online documentation. Open-sourcers: 1.2r2 is Subversion revision 3866 on the main trunk.

September 12, 2009: NVIDIA recently updated their 3D Vision for Quadro information page. If you are considering purchase of a 120 Hz LCD for use with PyMOL, please make sure you also secure an appropriate late-model Quadro graphics card. OpenGL-based Stereo 3D does not work on GeForce cards! Also note that support for 3D Vision is still limited to Windows only -- you cannot use 120 Hz LCDs for Stereo 3D under Linux or Mac OS X!
August 14, 2009: We have updated our free-but-placarded build of our ActiveX Control: AxPyMOL for playing PyMOL Session and Show files inside PowerPoint (Windows only).
July 23rd, 2009: nVidia today released updated and official Quadro drivers for Windows Vista and XP that enable use of PyMOL in stereo 3D on 120 Hz LCD displays. In addition to the latest drivers, you need a recent Quadro FX graphics card, a GeForce 3D Vision kit and either a ViewSonic VX2265wm or a Samsung 2233RZ LCD display (total cost: < 750 USD).
If you run Mac OS, Linux, or have a Windows laptop without a built-in Quadro chip, don't feel left behind -- get yourself a Zalman ZM-M220W 3D LCD instead (cost: < 300 USD)! No special graphics hardware or drivers are required to use PyMOL with Zalman displays, and the resulting stereo 3D effect is equally good on any platform.
July 16th, 2009: nVidia today released beta Windows graphics drivers that enable use of PyMOL in stereo 3D on 120 Hz LCD displays. In addition to the latest drivers, you need a recent Quadro FX graphics card, a GeForce 3D Vision kit and either a ViewSonic VX2265wm or a Samsung 2233RZ LCD display (total cost: < 750 USD). See our additional instructions regarding beta driver installation for Vista and Windows XP (NOW OBSOLETE -- SEE ABOVE).
July 9rd, 2009: Updated PyMOL 1.2r1 builds have been posted for Mac, Windows, and Linux. 64-bit builds for Windows and Linux are now included. Current PyMOL Subscribers may download version 1.2 builds directly or access them through online documentation. Open-sourcers: 1.2r1 is Subversion revision 3827 on the main trunk.

June 30, 2009: Schrödinger Announces PyMOL for Maestro plug-in Now Available

NEW YORK, NY (June 30, 2009) - Schrödinger announced today that in response to strong customer demand, it has partnered with Dr. Warren DeLano, PyMOL author and DeLano Scientific founder, to jointly deliver a 'PyMOL for Maestro' plug-in module. The plug-in is included with the latest Windows and Linux builds of PyMOL 1.2, and it provides for simple, one-click access to PyMOL from within Schrödinger's Maestro application. "It's been a real pleasure working with Warren, who's been a visionary and a committed leader in the open source community," said Schrödinger's President, Dr. Ramy Farid, "this plug-in provides our users instant access to all the power of PyMOL's graphics."

The plug-in is implemented as a Python script, which is invoked from Maestro, the graphical user interface for all of Schrödinger's computational programs. The script seamlessly launches PyMOL, automatically loading Maestro's current molecular content. "The quality of PyMOL's ray-traced images is without equal, and now with just one click, our users can also take advantage of PyMOL's comprehensive movie-making features, as well as its real-time, interactive 3-D presentation capabilities," adds Dr. Farid.

"This development enables users to more rapidly convert breakthrough computational models into compelling visual presentations," said Dr. DeLano, "I am excited that Maestro can now synergize with this increasingly ubiquitous open-source resource," Dr. DeLano adds while referring to PyMOL, "this new plug-in enables dissemination of Schrödinger-based scientific results out to the entire PyMOL user community as dynamic, interactive content."

The plug-in script is available from and supported by both companies; in addition to being bundled with PyMOL 1.2, it will also be available from Schrödinger's website. Reflecting on the development effort, Dr. DeLano says, "This was a fun project that will end up saving lots of time for lots of people. I enjoyed working with the Schrödinger team and look forward to our ongoing efforts to integrate open-source and commercial software in ways that will benefit all of our users."

You can read the full press release on Schrödinger's site.
June 30, 2009: PyMOL 1.2r0 builds have been released for Windows and Linux (32 bit).

What is new in PyMOL 1.2?

Version 1.2 Open-Source Code includes the following major enhancements relative to version 1.1:
1. Improved animation capabilities, with a movie timeline slider and automatic object motion path generation.
2. Improved 3D small-molecule builder, with support for the "mengine" open-source MMFF implementation.
3. Improved movie export, with support for the "mpeg_encode" open-source MPEG writer.
4. Support for new stereo 3D displays from Zalman, iZ3D, and Samsung (3D HDTV).
5. Selective surfacing of pockets and cavities (see Settings -> Surface menu).
6. Over 100 other minor tweaks, enhancements, and bug fixes implemented since the prior release.
Version 1.2 Incentive Builds include the following added benefits for project sponsors:
1. Bundled "RigiMOL" 3D structure morphing (see examples/rigimol folder).
2. Integration with Schrödinger's Maestro interface (and .MAE file reading -- see scripts/maestro folder)
3. A MSI-based Windows installer with improved Vista compatibility.
4. Convenient pre-compiled integration with the following open-source packages:
  python (2.5), numpy (1.3), apbs (1.1), mengine, mpeg_encode, and certain vmd-molfile-plugin readers (TRR, XTC, DCD, CUBE, ...).
MacPyMOL 1.2 builds and 64-bit builds for other platforms are still pending, but should be out within a week or two!
Click here to read older news items.

PyMOL Summary, Keywords, & Links: PyMOL is a molecular viewer, render tool, and 3D molecular editor developed in the spirit of RasMol and OpenRasMol and intended for visualization of 3D chemical structures including atomic resolution X-ray crystal structures of: proteins, nucleic acids (DNA, RNA, & tRNA), and carbohydrates, as well as small molecule structures of drug leads, inhibitors, metabolites, sugars, nucleoside phosphates, and other ligands including inorganic salts and solvent molecules. PyMOL serves academic research and education in chemistry and biology, and the biotechnology and pharmaceutical industries by rendering publication-quality journal illustrations of macromolecules including drug targets such as GPCRs, kinases (Abl, Raf, Aurora, EGFR), proteases (HIV, BACE, Factor Xa), phosophorylases (PTP1B), and other enzyme targets, as well as therapeutic biomolecules such as humanized antibodies, cytokines, hormones, and serpins. Available molecular representations for nanotechnology pictures include space-filling "CPK" atoms, chemical bonds, cartoon ribbons, molecular surfaces, and solvent accessible surface meshes. As a stereochemistry viewer, PyMOL can illustrate the 3D stereochemical relationships of organic chemistry. As a crystallographic protein structure viewer, PyMOL can display millions of atoms inside a crystal lattice. Molecular interactions can be represented using interatomic distances, van der Waals clashes, property-based, potential-based, & proximity-based coloring schemes, solid and mesh isosurface potentials, slice planes, and gradient field lines. PyMOL also supports input of electron density maps, electrostatic potential maps, and other volumetric data sets as well as arbitrary 3D geometries comprised of triangles, spheres, cylinders, cones, ellipsoids, and text. Output options include copy & paste, PNG images, QuickTime Movies (on Mac), VRML, Maya OBJ, and POVRay POV input files. Molecular animations can be created through simple object & camera motions or through input of trajectories from molecular dynamics simulations and other dynamic conformational ensembles such as 3D NMR structures, allosteric states, and Monte Carlo configurations. PyMOL can be scripted using Python and is available as both an ActiveX Control and a Java/JNI Component. PyMOL supports OpenGL hardware from nVidia (3D Vision), ATI/AMD, and Intel, with stereoscopic 3D graphics display on devices such as the Planar3D, Samsung SyncMaster 2233RZ, Viewsonic Fuhzion VX2265wm & PJD6220-3D, ZScreen, and Christie MIRAGE with stereo 3D glasses or goggles. PyMOL integrates with the open source projects: APBS, mengine, and mpeg_encode via the FreeMOL open-source compilation, and can read PDB (protein data bank), PQR, MOL, SDF, MOL2, XPLOR, CCP4, DSN6, DX, TRJ, DCD, XTC, and GRID formatted files. PyMOL also integrates with the SEURAT data mining & collaboration tool from Synaptic Science and can read molecular modelling files written by Chemical Computing Group's "MOE" (Molecular Operating Environment), as well as Schrödinger's Maestro suite.

The PyMOL open-source code is hosted at: