The father of PyMol died recently - He will always be remembered

I am a cell biologist, but I know PyMol and use it rather frequently. The father of PyMol, he will truly be remembered.

News from MacResearch

In Memoriam: Warren L. DeLano

By dgohara at Thu, Nov 5 2009 8:23pm

It's with sadness that I bring the news that Warren L. DeLano passed away, suddenly and unexpectedly, on Tuesday November 3rd. For some of you, Warren's name will be instantly recognized. For many more, you know him indirectly as the developer of PyMOL. PyMOL, the open source software he began developing as a graduate student, would eventually become his life's work and has become one of the key tools used by structural biologists the world over.

In time, PyMOL would be used by a wide variety of scientists, that would embody one of the most unique cross-sections of scientific endeavor. Noted for it's ease of use for the novice, yet possessing a rich set of features and powerful scripting options for advanced user, PyMOL quickly became the de facto standard for the generation of publication quality images and as a tool for molecular analysis and visualization.

As a contributing developer of a third-party plugin to PyMOL I had the opportunity to interact with Warren quite often. It wasn't until 2006 that we were finally able to meet in person. Our first face to face conversation took place at no other than the scientific poster session at Apple's Worldwide Developers Conference. Instead of standing by our posters we talked the entire session. At the time, Warren was focusing on building his business. We talked quite a bit about the trials of finding the right business model and developing new functionality that would enhance the usefulness of PyMOL.

After the session concluded, Warren joined myself and the other MacResearch members for drinks at a watering hole across the street from our hotel where the conversation covered a variety of topics and personal interests. For the next few years I would always bump into Warren at WWDC. You could always tell it was Warren from a distance, because he had always had a huge smile on his face, and a spring in step.

Warren was a passionate and heavy advocate for the principles of open source software. He helped build a large community of PyMOL using scientists, many of whom would contribute utilities to help enhance the feature set of the application. Always helpful, Warren became known for his willingness to answer questions, listen to user feedback and provide assistance on the PyMOL mailing list.

It's unfortunate and untimely events such as his passing, that serve as reminder of the importance to not allow the petty and insignificant annoyances in life consume us. Tomorrow is promised to no one. Yet, we can only hope that in our lifetimes, we will contribute as much to the forward progression of science as Warren has. Warren built a legacy that continues to grow with each use of his software and every discovery it helps contribute to. Although he is no longer with us, Warren will always be remembered.

What is PyMol? More details please visit pymolwiki

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), Caspase, Cathepsin, 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.

PyMOL is Good for:
1. Viewing 3D Structures
2. Rendering Figures
3. Giving Presentations
4. Animating Molecules
5. Sharing Visualizations
6. Exporting Geometry