PyMOL Archived News Items

PyMOL Achived News Items

August 21, 2008: Another PyMOL-based Cover: McGeehan et al. Structural analysis of the genetic switch that regulates the expression of restriction-modification genes. Nucleic Acids Research, 2008, Vol. 36, No. 14 4778-4787.
August 18-20, 2008: DeLano Scientific LLC hosted booth #835 at the American Chemical Society Expo in Philadelphia, PA. Thanks to everyone who stopped by!
July 14th, 2008: The PyMOL 1.1 open-source code is now branched from trunk as "b11" in the Subversion repository. Trunk will now contain 1.2 beta code, so version 1.1 open-source code may be checked out using the following command:
```
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/branches/b11/pymol pymol-1.1
```
July 3rd, 2008: The PyMOL 1.1 build set is complete and includes 64 bit builds for Windows and Linux. Current PyMOL Subscribers may download version 1.1r1 builds directly or get them through official documentation.
June 26th, 2008: Linux is now our #1 recommended platform for stereo 3D visualization with PyMOL, and Microsoft Windows is our #2. Due to unresolved OpenGL stereo 3D composition issues inside of Mac OS X Leopard, we cannot currently endorse purchase of Apple computers for scientific visualization tasks which specifically require stereo 3D. Of course, octa-core Mac Pros are still great for lots of other things, such as ultra-fast parallel ray tracing or running multiple operating systems simultaneously using VMware or Parallels!
June 24th, 2008: MacPyMOL 1.1 is now available for direct download or via the official documentation.
June 1st, 2008: The PyMOL 1.1 release process has begun! Current PyMOL Subscribers may download version 1.1r0 builds for Windows and Linux and a prerelease build for Mac OS X. New builds can also be obtained via official documentation. The complete 1.1 build set should be available by the end of the month.
April 18, 2008: Another Recent PyMOL-based Cover: Taylor et al. Allosteric Motions in Structures of Yeast NAD+-specific Isocitrate Dehydrogenase J. Biol. Chem..2008; 283: 10872-10880.
April 7-9, 2008: PyMOL author Warren DeLano will join partner Synaptic Science LLC in booth 427 at the American Chemical Society Expo in New Orleans, LA. You are invited to come see how we are integrating PyMOL with SEURAT to help scientists share and use 3D molecular structures within the full informational context of drug discovery programs.
March 6th, 2008: A BETA build of the PyMOL ActiveX Control (See PowerPoint DEMO) is now available to major industrial sponsors willing to fund and participate in the final work-up of this exciting new Incentive Product. Interested? Please email sales@delsci.com for an AxPyMOL BETA quote. Otherwise, stay tuned: AxPyMOL will be standard with all PyMOL Subscriptions starting in early 2009, if not sooner!
January 3rd, 2008: PyMOL 1.1 beta 3 executable builds have been posted for download by current PyMOL Subscribers. Builds are also accessible via the Official Documentation. Key improvements include improved Windows Vista compatibility, anisotropic temperature factor ellipsoids, and better scene-to-movie support. (1.1b3 is svn trunk rev. 3143).
fetch 1ob7,async=0; show ellipsoid
December 31, 2007: Recent PyMOL-based covers: Multiple articles on P-type ATPases in Nature 450 pp. 957, 1036, 1046, 1111, 1505-1516. and Rosette M. Roat-Malone Bioinorganic Chemistry: A Short Course, 2e. Published by Wiley.
November 23, 2007: More PyMOL-based journal covers: Luc Bonnefond et al Aminoacyl-tRNA Synthetases from Human Mitochondria. Structure 15(11) 1505-1516. and Vadim Cherezov et al. High-Resolution Crystal Structure of an Engineered Human Adrenergic G Protein Coupled Receptor Science 318(5854), 1258-1265.
November 2nd, 2007: Free JyMOL 0.7.1 Evaluation Builds have been posted for download by Java developers. JyMOL is a Java/JNI-based variant of the PyMOL molecular graphics kernel. This download may be of interest to developers of multi-platform Java applications (but not applets) for biology and chemistry.
October 4th, 2007: DeLano Scientific has moved! We have relocated from temporary space into our new office at 540 University Ave., Suite 325, Palo Alto, CA 94301. Although this should be a long-term home, for ordinary postal mail, please continue to use P.O. Box 1118, Palo Alto, CA, 94302-1118, USA.
September 20th, 2007: Yet another PyMOL-based journal cover: Structure of acid-sensing ion channel 1 at 1.9 A resolution and low pH. Nature 449 (7160) 316-323. Jayasankar Jasti et al.
September 18th, 2007: A PyMOL 1.1 beta 2 executable for Windows Vista has been posted for download by current PyMOL Subscribers. Please provide feedback on how well this release runs on your new PC (please also tell us your graphics processor type!).
August 31st, 2007: PyMOL 1.0 revision 2 executables have been posted for download by current PyMOL Subscribers. Contains Minor fixes and updates only. Source code:
```
svn export https://pymol.svn.sourceforge.net/svnroot/pymol/tags/1.0r2/pymol pymol-1.0r2
```
August 20-22, 2007: DeLano Scientific LLC hosts booth 449 at the American Chemical Society Expo in Boston, MA.
August 17, 2007: PyMOL 1.1 beta 1 builds released to subscribers for Windows and Mac platforms. This version is better at finding polar interactions between proteins and ligands when using "stock" PDB files from the wwPDB (which STILL lack bond valences, ugh!).
August 7-8, 2007: DeLano Scientific LLC is exhibiting inside the Apple booth (#512) at the Drug Discovery Today in Boston, MA.
July 31st, 2007: PyMOL 1.0 revision 1 executables have been posted for download by current PyMOL Subscribers. If you already have revision 0, there is no need to upgrade unless you are using PyMOL to share .MOE files.
July 10th, 2007: The PyMOL 1.0 open-source code is now branched off trunk as "b10" in the Subversion repository. Trunk will now contain 1.1 beta code.
```
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/branches/b10/pymol pymol-1.0
```
June 21st, 2007: PyMOL 1.0 executables have been posted for download by current PyMOL Subscribers.
May 23rd, 2007: PyMOL 0.99rev10 executables posted for download by current PyMOL Subscribers. The open-source code for 0.99rev10 is revision 2974 of branch "b099" in the Subversion repository. This release contains minor bug fixes relative to 0.99rev8 and 0.99rev9.
April 12th, 2007: DeLano Scientific LLC presenting at the NIH as part of Molecular Modeling, Computational Chemistry, Pathway Analysis on a Mac.
March 28th, 2007: PyMOL & DeLano Scientific LLC covered in Biocomputation Startups: Where Does Value Lie? under "The Open Source Business Model" (5th page of linked PDF).
January 14, 2007: Updated PyMOL 0.99rev8 Executable Builds have been posted for download by current PyMOL Subscribers.
The open-source code for 0.99rev8 is revision 2805 of branch "b099" in the SVN repository.
```
svn export -r 2805 https://pymol.svn.sourceforge.net/svnroot/pymol/branches/b099/pymol pymol-0.99rev8
```
Updated Educational-use-only PyMOL Builds are also now available upon approval at no cost to teachers and full-time students.
If you need updated download credentials, please contact sales@delsci.com with your invoice number, a subscription quote request, or an educational use declaration.
November 1st, 2006: DeLano Scientific LLC is moving! The new office address is:

DeLano Scientific LLC
Suite 541-F Cowper St.
Palo Alto, CA 94301-1803, USA

Please use the above address for Fedex, DHL, and other private courier services.

For U.S. Mail and international postal services, please use:

DeLano Scientific LLC
P.O. Box 1118
Palo Alto, CA 94302-1118, USA

Updated contact numbers:
Business: +1-650-283-6945
Fax: +1-650-989-4082
Cell: +1-650-346-1154 - for PyMOL Support Subscribers & Open-Source Developers only please!
September 1st, 2006: Learn more PyMOL at the American Chemical Society Meeting! Lead PyMOL Developer Warren L. DeLano will be holding an informal PyMOL demonstration, training session, and users group meeting in Booth #327 of the ACS National Exposition in San Francisco, September 11th-13th. Please stop by at your convenience!
August 1st, 2006: DeLano Scientific has adopted a controlled-access download system for our most current precompiled PyMOL builds (including betas). Going forward, access to these convenient and ready-to-run executables will be limited to project sponsors only. Non-sponsors can of course continue to compile the updated Open-Source code at no cost (other that time and effort) or use our older precompiled builds.

If you are a current PyMOL Subscriber and have not yet received your new download credentials, please email sales@delsci.com with your most recent invoice number and subscription expiration date. We will then send you your updated download credentials as soon as possible!
July 1st, 2006: Operations Manager Joni Lam has completed her time with the company and is taking the next step in her career. DeLano Scientific thanks her for her contribution to the PyMOL project and wishes her luck in future endeavors!
February 6th, 2006: PyMOL v0.99 release candidates are out! Download a precompiled executable for Windows, Mac, Linux, IRIX, or Solaris, or compile the open-source code.
February 5th, 2006: DeLano Scientific announces immediate availability of the MacPyMOL Universal Binary for Intel/PPC Macs, and posts various benchmarks showing that PyMOL runs almost as fast on an entry-level iMac Core Duo as on a much more expensive dual-processor Opteron Linux workstation.
January 9th, 2006: PyMOL 0.99 is Coming Soon! Please test the latest 0.99 beta build and provide immediate feedback on any serious problems you encounter so that they can be corrected prior to the official release.
October 21st, 2005: Updated information on purchasing stereo 3D hardware & displays can be found here.
October 19th, 2005: Apple releases the first PowerMacs that support for Stereo 3D "in a window". MacPyMOL builds that fully exploit this capability are now available.
July 18th, 2005: Sequence to Structure (S2S): display, manipulate, and interconnect RNA data from the sequence to the structure (Fabrice Jossinet) -- A new Java tool that uses PyMOL for molecular visualization.
May 2nd, 2005: PyMOL v0.98 has been released. Click here to download a precompiled PyMOL Executable Build (Windows, Mac OS X, Linux, IRIX, or Solaris) from DeLano Scientific LLC .
March 28th, 2005: PyMOL S.F. Bay Mailing List: Are you local to the San Francisco Bay Area? If so, then please subscribe to the Yahoo pymol-sfbay mailing list in order to be notified of local PyMOL events.
February 16, 2005: The PyMOL Wiki Goes Live! Much thanks to Jason Vertrees for creating this important community resource for PyMOL users.
February 10, 2005: Review: DeLano W.L. The Case for Open-Source Software in Drug Discovery. Drug Discovery Today, 10, 213-217 (2005) is now available online via ScienceDirect. No subscription? Request a reprint from the author.
January 14, 2005: PyMOL version 0.98 is nearing completion! If you haven't yet tried one of the latest 0.98 beta versions yet, then please do so soon and provide feedback. Builds are available for Windows, Linux, and IRIX as well as for Mac OS X. Or you can simply pull the current source from CVS.
January 13, 2005: Does Stereo 3D Matter to You? DeLano Scientific LLC is collecting virtual "signatures" by email from those who rely upon OpenGL Stereo 3D visualization. Why? Because Apple hasn't implemented industry-standard stereo 3D (in a window) into Tiger, their new MacOS X release 10.4, even though every other major platform already supports this capability. We will hand-deliver a hardcopy to Apple management of every email we receive on this issue before February 1st in order to emphasize how much this feature matters to scientists and engineers today. Click here to read and respond to the full petition. Thanks!
January 12, 2005: DeLano Scientific LLC officially announces the opening of its South San Francisco office!
```
   DeLano Scientific LLC
   400 Oyster Point Blvd., Suite 213
   South San Francisco, CA 94080-1918, USA
   V: 650-872-0942   
   F: 650-872-0273
```
x Please make an appointment to stop by for lunch if you're in town! We'll soon be holding regular users meetings and training sessions for local PyMOL users and out-of-town guests.
July 15, 2004: Open-Source PyMOL 0.97 has been released for all platforms. This version addresses a serious bug in the version 0.96 sequence viewer and includes two useful new plugins, for APBS electrostatics calculations and direct PDB downloading.
July 14, 2004: Some users have discovered the new Plugin interface in PyMOL 0.96. Feel free to write your own, and submit them for inclusion on the new plugins page!

July 12, 2004: Open-Source PyMOL 0.96 has been released for all platforms. New features include:

   - Sequence viewer for sequence-based manipulation of 3D molecules.
   - Experimental vacuum electrostatic potential calculations for proteins (only).
   - Get view button now copies matrix to clipboard automatically.
   - MOL2 and multi-MOL2 file input.
   - Display of aromatic bonds from SDF, MOL, and MOL2 files.
   - New selection keywords: polymer, solvent, organic, inorganic.
   - APBS interoperativity: PQR file input and output, DX file reading.
   - Plugin Menu for end-user add-ons.
   - Molecular picking and editing is now more general.
   - Improved surface_quality=2.
   - New "surface_solvent" setting allows display of solvent accessible surfaces.
   - Improved color rainbow.
   - Various other minor features have been added
   - Various major and minor bugs have been fixed.

May 3, 2004: Luca Jovine releases NUCCYL 1.4 for PyMOL.

April 3, 2004: PyMOL 0.95 has been released for all platforms. An official 0.95 release of the MacPyMOL Incentive Product for OS X is also available for download. New features include:

   - Presets (in the Action menu) provide common views very quickly.
   - Context-specific pop-up menus now direct actions to where you point.
   - Mouse wheel can now control clipping slab width and position.
   - Improved look-and-feel, including bigger controls and longer names.
   - Appearance wizard facilitates color and representation control.
   - Labels can now be ray traced, with a few new fonts (label_font_id=0,1,2,3,4).
   - Two new surface types: dots (surface_type=1) & tri-mesh (surface_type=2) added.
   - Better handling of alpha-channel for semi-transparent figures.
   - Cartoons and spheres can now be "picked" using the mouse.
   - Roving origin behavior has been improved.
   - New cross-platform build for OS-X uses Tcl/Tk under X11 without Fink.
   - Molecular picking and editing is now more general.
   - Numerous features and tweaks have been added.
   - Various major and minor bugs have been fixed.

(3/22/2004) Updated beta test versions of PyMOL 0.95 for Windows, SGI/IRIX, and Linux as well as the native MacPyMOL Incentive Product for OS X are available for download. As always, please exercise caution with test versions.
(3/6/2004) Updated beta test versions of PyMOL 0.95 for Windows and Linux as well as the native MacPyMOL Incentive Product for OS X are available for download. As always, please exercise caution with test versions.
(2/5/2004) Sponsors and prospective sponsors running Mac OS X may now download beta versions of the MacPyMOL Incentive Product from DeLano Scientific (last updated 2/21/2004 -- Judges, what do you think? ). Synchonized beta builds of the Open-Source equivalent for Windows and Linux are available too (standalone builds only). As always, please exercise caution with test versions.
(11/1/2003) PyMOL 0.93 has been released for Windows, Linux, G4 Macs, G5 Macs, SGIs, Suns, and as Source Code. This release fixes several problems which immediately became apparent with last week's 0.92 release (see below for new features in that release).
```
   - Fixed blunder with O/BRIX map reading code.
   - Fixed 0.86 session reading.
   - Adjusted Z-axis tracking of the roving origin to clipping planes movement.
   - Changed default save location for PNG files under OS X (avoids confusion).
```

(10/27/2003) PyMOL 0.92 has been released for Windows, Linux, G4 Macs, G5 Macs, SGIs, Suns, and as Source Code. There are also special RedHat RPMS and Windows binaries that will enable you to "import pymol" from external Python code in order to use PyMOL as a simple viewer module.

This is mostly an "under the hood" improvements release, but there are some developments worth noting:

Significant changes

- New "dss" command assigns secondary structure quickly.
- PyMOL can now read O maps (BRIX but not DSN6) and some Biosym GRiDs maps.
- Improved ray tracing quality and speed.
- Long lists of residues in selections are now allowed.

Other changes

- New "import pymol" support for RPM & Win32 builds that use system Python.
[Don't forget to call pymol.finish_launching() afterwards though!]
- Improved alpha-channel support for transparent surfaces and backgrounds.
- API's "cmd.do" can now take multi-line strings and lists.
- New "split_states" command for separating NMR ensembles.
- New "cartoon_transparency" setting.
- Can display bond valences while in stick mode.
- New "stick_ball", "stick_ball_ratio" settings for ball & stick models.
- Gaussian map generation from model coordinates.
- Can preserve original PDB atom IDs (pdb_retain_ids) & order (retain_order).
- Much much faster loading of multi-model PDB files and trajectories.
- Deuterium and Calcium handling improved.
- New "set_symmetry" & "get_symmetry" commands.
- Mutagenesis wizard preserves cartoons.
- New "get_pdbstr" API function.
- New "movie_loop" setting can disable looping.
- Sculpting engine now aware of simple sp3-sp3 torsions.
- Finer Z-scaling/movement control.
- Upgrade facility for secure enterprises running Windows.

(9/5/2003) PyMOL 0.91 with Demonstrations has been released for the Apple Power Macintosh G5. This release includes a collection of real-time PyMOL animations which celebrate the performance of Apple's fast new computer system. Recent optimizations for G5 hardware have more than doubled the antialiased ray-tracing speed over non-optimized versions. Dual-processor Macintosh users will realize an additional 180% boost in rendering performance from multiprocessing. OpenGL, molecular sculpting, and surface calculation code have all been tuned using Apple's fantastic CHUD tools to deliver maximum performance on Apple hardware. Current Power Macintosh G4 users will benefit from many of these tweaks as well.
(6/30/2003) PyMOL 0.90 has been released for Windows (7.5 MB), Linux (9.3 MB), OS X (20.9 MB), and IRIX (10.2 MB). In addition to fixing the bugs in version 0.88, PyMOL 0.90 supports faster rendering, faster partial surface calculations, and multiprocessing. Click here for more download options.
(6/9/2003) PyMOL 0.89 has been released for Windows (only). This is a bug-fix release. The previous release was unable to read session files written by itself under Windows. Version 0.89 does not suffer from this problem.
(6/1/2003) PyMOL 0.88 has been released for Windows, Linux, OS X, and IRIX. Lots of great new features -- but be warned that new documentation is minimal! Check out the updated Demonstrations for an quick tour.

Some of the new features include:

   - Standalone installer for Windows (no external Python required)
       ***heavily requested by corporate IT groups***
   - CMYK color support ("space cmyk" much better for publications)
   - Roving detail/density modes (hard to explain -- best seen)
   - Improved transparency for surfaces
   - Cartoon highlight color (ala Molscript)
   - Opaque/solid objects in ray_tracer 
   - Spectrum command for fast color ramps
   - Electrostatic map reading (.phi format) and graphic color ramp gadget 
   - Wizards now saved in session file
   - Wizards now stack
   - Scenes (more powerful than views; more convenient than sessions)
   - Updated demonstrations
   - Single click-and-drag rotation of bonds in editing mode
   - Tear off menus
   - Stereo support on Mac (native version only) 
   - Improved performance on certain tasks (rainbow, color by chains,color by b-factor)
   - Better support for stereo figure generation with "ray angle=-3",
        "ray angle=3" etc

(4/18/2003) Accelerated OpenGL Hardware Recommendations (updated 4/30/2003): As we recently updated our development systems, we had a chance to obtain and test some exciting new graphics hardware! Thus, we can now provide the following endorsements:
- For monocular visualization under Windows, we recommend the ATI Radeon 9700 Pro (approx. $400). This is by far the fastest OpenGL engine we have ever seen PyMOL run on!
- For stereo visualization under Windows, we are re-evaluting our recommendation of the nVidia Quadro4 750XGL (approx. $500) because we and other users have encountered image stability problems (on Windows only!).
- For monocular visualization under Linux, we recommend the ATI Radeon 8500 (approx. $200). This high-performance card is now supported out-of-the-box with full OpenGL acceleration under RedHat 9.0 (XFree86 4.3) -- no manual configuration is required!
- For stereo visualization under Linux, we recommend the ATI FireGL2 (approx. $600). It is not the fastest card in the world, but IT SIMPLY WORKS. If you need better performance, go with the nVidia Quadro4 750XGL, but be prepared for driver updates.
- For stereo visualization under Mac OSX, we recommend the nVidia GeForce4 Titanium (approx. $400). However, we would expect even better performance from the ATI Radeon 9700 (not yet tested).
- For monocular visualization on a laptop, we recommend the nVidia GeForce4 Go 460 chip running under Windows. However, we also expect excellent performance from the ATI Mobility Radeon 9000 chip, which will likely do better with smooth (antialiased) lines.
These are the graphics configurations which we are likely to be using for PyMOL development over the next year or two, so you may want to consider purchasing the same (or very similar) hardware in order to be certain that PyMOL will run optimally on your system. When in doubt, choose ATI over nVidia. ATI is currently more Linux-friendly and supports hardware antialiased lines on most of their cards (desirable for working with electron density!).

If you must use nVidia cards with Linux, I suggest trying RedHat 7.3 -- there are some serious problem with nVidia's latest driver (1.0.4349) on RedHat 9.0 (which shipped with broken C libraries). Also try to avoid nVidia's nForce chipsets -- thanks to their propriety architecture, you can't use non-Vidia AGP graphics cards with them under Linux!
(4/3/2003) It's for real! DeLano Scientific LLC has begun full-time development, documentation, and support of PyMOL. The project is no longer a part-time hobby, but rather the means by which we will demonstrate the benefit of an Open-Source approach to the business of scientific software.

PyMOL's principal developer, Warren L. DeLano, Ph.D., has left his position at Sunesis Pharmaceuticals and will be focusing intensively on the project in order to expand documentation, usability, interface, and capabilities while directly helping PyMOL users get the most out of the package.

If you have not yet purchased a PyMOL license, then please do so now in order to sponsor the project at this critical time. Please learn what we are about and promote low-cost Open-Source scientific software by helping us to become self-sustaining. Thank you!

We are also pleased to announce that PyMOL maintenance agreements now include user support. If you are an existing license holder, please consider purchasing an annual maintenance agreement in order to renew your sponsorship of the project and to access this new offering.
(2/14/2003) Apple Computer and StereoGraphics Corporation have demonstrated PyMOL running in STEREO 3D on an OS X Mac in their booth at the annual meeting of the American Association for the Advancement of Science. The version they are showing is pre-release, but can be obtained upon request, if you have an OS X stereo hardware setup with "blue-line" sync capability. To purchase such a setup, contact Stereographics directly.
(1/14/2003) Keep your eyes out for PyMOL cover illustrations in coming months -- several are reportedly in the pipeline. The first one of the year can be found on Wiley's January 2003 issue of Chembiochem, which uses PyMOL surfaces and rendering in an illustration.
(1/8/2003) A full-featured, accelerated version of PyMOL for OSX Macs is now a reality! Apple's new beta X11 release allows Mac users to fully access their OpenGL hardware under 10.2.3, thus blowing open the wide world of X11/OpenGL software (such as PyMOL) to Mac users. Follow Yuriwho's instructions or Bill Scott's instructions in order to get PyMOL running faster on your mac. Special thanks to Yuriwho and Bill for sharing this information, and thanks to the Fink group for the OSX port. (WARNING: a high bandwidth connection is required to download the up to 400 MB(!) of packages you may need, and do give yourself a couple hours to learn the ropes if you are new to Fink (as I was). BE SURE to install all of the binary dependencies you'll need (python, etc.) before compiling pymol, otherwise you'll spend forever compiling those other packages unnecessarily.
(1/3/2003) PyMOL 0.86 has been released with precompiled binaries for Windows, Linux, and IRIX. PyMOL now supports Session Saves! Download your copy today. A Mac OSX update will come soon.
(11/10/2002) The PyMOL project has reached an important milestone. Thanks to your donations and license purchases, we are now able to retain the first independent contractor to work on PyMOL! A technical writer is now working part-time on the PyMOL manual. If all goes well, then improved PyMOL documentation should start to become available in coming months.
(11/9/2002) Chris Oubridge and Luca Jovine have released an example PyMOL movie with the associated PyMOL script used to generate it (WARNING: high bandwidth required).
(11/8/2002) Kristian Rother has created yet another excellent PyMOL page. It is a collection of tips gathered from the PyMOL mailing list. Thank you Kristian, this will greatly help PyMOL users!
(10/28/2002) In a recent email exchange on the mailing list, Warren articulates his current vision for PyMOL/iPyMOL, and his thoughts regarding what it will take to bring good open-source molecular modeling software into existence.
(9/9/2002) Jim Hu has created a MacOSX-specific adaption of Carly Huitema's PyMOL Tutorial . Thanks Jim -- I'm sure your efforts will be appreciated by many.
(9/2/2002) A second beta-test version of the native, hardware-accelerated MacOSX version of PyMOL has been released. This version works fine under 10.2 as well as 10.1. Still lacking is the standard menu bar, but more of the pieces have fallen into place. WARNING: this is nearly a 40 MB file download (pymol-0_84beta-bin-osx.dmg.gz).
(9/1/2002) Please read this important announcement regarding PyMOL's future. In summary, PyMOL will soon be joined by a companion low-cost commercial add-on, Incentive PyMOL (iPyMOL), which will be used to build a sustainable funding source for all PyMOL development. This enhanced version will only be available to active PyMOL supporters, included existing PyMOL licensees. You may wish to lend your support to PyMOL soon in order to avoid higher license fees for iPyMOL. However, do expect the open-source version of PyMOL to continue improving far into the future, since it will be the core visualization engine behind iPyMOL.
(8/1/2002) A new mailing list has been created for discussion of general scientific topics related to PyMOL The "pymol-science" mailing list [PyMOL-Sci] will have broad coverage of molecular modeling, X-ray crystallography, computational chemistry, informatics, structural analysis, and any other areas in which PyMOL has some utility. The list will also cover scientific software needs and available solutions which extend beyond PyMOL.
Meanwhile, the "pymol-users" mailing list [PyMOL] will continue as a highly focused forum for sharing tips on how to use PyMOL more effectively.
(7/18/2002) PyMOL's user group mailing list now reaches 200 subscribers! There are twice as many PyMOL users today as there were six months ago, and together we are building an active peer-to-peer support community via the mailing list. Come participate in the open-source molecular software revolution!
(6/27/2002) A Painless PyMOL Install for Linux can hopefully be achieved with a special 0.83 version release: .
1. Follow this link to download pymol-0_83-bin-linux-libc6-i386.tgz
2. tar -zxvf pymol-0_83-bin-linux-libc6-i386.tgz to create the pymol directory.
3. cd pymol
4. ./setup.sh to create "pymol.com".
5. ./pymol.com to start up PyMOL as a test.
6. Successful? then link or copy "pymol.com" to "pymol" in some "bin" directory in your path (for instance $HOME/bin):
  cp pymol.com $HOME/bin/pymol
  You should now be able to run PyMOL from any location.
(6/20/2002) A Short PyMOL Tutorial has been prepared by Carly Huitema. Thank you Carly! (the master copy can be found at Tripod, but beware of annoying pop-up advertisements.)
(6/16/2002) Version 0.82 has been released! Relative to 0.80, this is mostly a bug fix and minor improvements release, but there are a couple of new features, such as cross-eye stereo and some additional operators in the selection language (within/of, present, state). Binaries are available for Windows, Linux, and IRIX. Hopefully, the native MacOSX port will soon follow.
(6/10/2002) Hardware Stereo 3D under Linux! I have personally confirmed that PyMOL performs well with quad-buffer hardware stereo under Linux. Thus, I can now recommend the following configuration, which also works well with the absolute latest version of O (8.0.8):
- Linux RedHat 7.1
- ATI FireGL2 (unfortunately expensive, and now special-order only).
- Exact drivers: fgl23glk-glc22-4.0.3-1.9.7.i586.rpm + fgl23ddx-glc22-4.0.3-1.9.7.i586.rpm
  http://www.ati.com/support/drivers/firegl/linux/cert/linuxfiregl4certx403197.html
  Other versions may work, but these are the only RPMs which functioned in my hands.
- Affordable emitters and glasses can be found at www.nuvision3d.com.
- An untested graphics alternative would be to use a Radeon 8500 card with the XIG driver and a suitable emitter adapter.
(5/24/2002) Thanks to recent backing from several top pharmaceutical and genomics companies, DeLano Scientific has met 25% of the 2002 fundraising goal for ongoing PyMOL development. If you are in a position to commit funding in support of open scientific software, then please consider becoming a sponsor or licensee in coming months so that we can continue on track towards the goal of making PyMOL self-perpetuating! (contact: warren@delanoscientific.com). With your help, PyMOL will continue to thrive as an enduring and independent project that can be used by everyone in viewing molecules, from high-school students up through college professors and industrial research scientists.
(5/16/2002) First publication of a PyMOL image in Nature. Hariharan Jayaram, Zenobia Taraporewala, John T. Patton, B. V. Venkataram Prasad. "Rotavirus protein involved in genome replication and packaging exhibits a HIT-like fold." Nature 417, 311-315 (2002). They used PyMOL in conjunction with Molscript ribbons in order to generate a transparent surface representation (Figure 1b) Thanks for the acknowledgement (under structure determination and refinement)!
(4/9/2002) Version 0.80 has been released! However, since this version hasn't been extensively tested, I'm holding off on building binaries for platforms other than Windows for in order to see whether or not problems surface (UPDATE: a few problems did surface, so the next multi-platform binary release will be 0.82).
(3/8/2002) A recent anonymous question came in regarding display of Bulgarian maps. Many of you will surely be relieved to learn that, Yes, PyMOL can indeed display Bulgarian Maps should the need arise. Just convert your Bulgarian map into "png" format prior to attempting this challenging feat, and then issue the carefully chosen commands:
```
viewport 650,650 
load_png bulgaria.png
```
(2/20/2002) PyMOL's mailing list now reaches over 100 subscribers! Thanks to each of you for sticking with PyMOL through the early days.
(2/17/2002) Funding via PayPal: Have you heard about PayPal's recent IPO? PayPal provides a safe way to send money online. You can try PayPal right now by making a PyMOL contribution via credit card.
(2/12/2002) PyMOL's first cover illustration! DeLano, WL. "Unraveling hot spots in binding interfaces: progress and challenges" Current Opinion in Structural Biology 12, 14-20 (2002). Please send me an email if you would like a copy of the PDF.
(2/9/2002) What is "molecular sculpting"? Molecular sculpting is NOT a realistic simulation and involves neither minimization nor dynamics. Rather, it is an iterative constraints optimization (like Shake or Rattle) designed to maintain atomic geometry and prevent van der Waals overlap. Molecular sculpting enables you to drag atoms and fragments in real-time using the mouse while preserving chemical geometries!
Molecular sculpting permits coarse molecular modeling instantly on any kind of structure. It will likely be useful for qualitative projects, such as medicinal chemistry brain-storming within the context of a co-complex structure, and for setting up molecular geometries for subsequent calculations using rigorous external tools (such as GAMESS, MacroModel, MOE, ICM, CCP4, X-PLOR, CNS, etc.).

To do molecular sculpting like in the video, paste the following commands into a ".pml" script:
```
set sphere_transparency,0.60
set sphere_color,white 
set auto_sculpt,1
mouse three_button_editing
fragment benzene
show sticks
show spheres
zoom all,4
```
Launch PyMOL, run the script from the File menu, then CTRL-left-click to drag atoms, or CTRL-middle-click to start building off of hydrogens...
(2/8/2002) The latest CCP4 Newsletter includes an article, "PyMOL: An Open-Source Molecular Graphics Tool", which provides a good introduction to PyMOL and is current as of PyMOL 0.68.
(2/6/2002) Version 0.78 has been released. This is the first release to include RPM packages for Linux, and it is the first release of PyMOL to include a real-time molecular sculpting feature.
(2/2/2002) A reminder for MacOS-X users: The GNU/Darwin version of PyMOL maintained by Michael Love is still the only functioning version of PyMOL available for the Mac. However, I have finally found a hardware sponsor to enable the native port, and it should be available within the next 2-3 months.
(10/18/2001) Low cost stereo graphics (<$200) on a Windows PC is attainable if you have an nVidia GeForce2 or 3 with stereoglasses. Read more...
(10/17/2001) A PyMOL mailing list has been created. Sign up if you would like to be a member of the PyMOL Users Group.
(10/8/2001) Apple's science and technology group released a short two-page story about PyMOL and other crystallography programs which run on Mac OS X with GNU/Darwin. A faster (OS X native) version of PyMOL will be available soon, but you should download and start using the GNU/Darwin version of PyMOL now, since portions of that will be required anyway...

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