Anders, Yes, we do have a long list of suggestions for PyMOL improvements, but many of them require a detailed understanding of PyMOL's fragile C-language internals, the study and modification of which is too much for Summer of Code. Also, in addition to the ActiveX effort just announced, some of the PyMOL-specific ideas have already been contracted and/or implemented.
My view is that the obvious low-hanging fruit for Open-Source PyMOL is integration with other open-source code. Since that mostly involves work at the Python level, such projects are well within the reach of students, especially if they have experience with both packages. So from where I sit, the obvious open-source candidates are: APBS (electrostatics -- improve the current plugin) RDKit (cheminformatics, depiction, UFF cleanup, etc.) mengine (MMFF small molecule cleanup) mpeg_encode (MPEG movie production on Linux, etc.) GIMP (image manipulation) Blender (general-purpose 3D modeling & animation) Jmol (publishing visualizations inside of web pages) Firefox (ditto) MMTK (molecular mechanics -- Python/flexible) GROMACS (molecular mechanics -- C/fast) OpenOffice (escape from the microsoft hegemony) (NOTE: work is already underway for mpeg_encode and mengine...) Are there other key open-source packages we might specifically target for integration with PyMOL, either through SOC or beyond? Although there are many niche tools, from a prioritization standpoint, efforts should focus on integrations that will impact the largest potential user base. So what hypothetical integrations would be useful to virtually all medicinal chemists, all structural biologists, all movie-makers, all paper-writers, and so on? Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info > -----Original Message----- > From: Anders Norgaard [mailto:anders.norga...@gmail.com] > Sent: Wednesday, March 05, 2008 1:10 PM > To: DeLano Scientific > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Will Pymol participate in Google Summer > of Code 2008? > > On Wed, Mar 5, 2008 at 9:57 PM, DeLano Scientific > <del...@delsci.info> wrote: > > Anders, > > > > No plans at present, but hey, it is still one whole week before a > > week before the deadline! > > :o) > > > Anyone out there with sufficient bandwidth to mentor? > > Hmm... Perhaps a nucleating effort on Jmol / PyMOL interporability > > would make a good SOC project? > > Well, there is also a whole list of stuff in your "PyMOL "By > Popular Demand" Survey (Jan 2008)" mail, perhaps some of > these could be bundled into a project? > > - An ActiveX Control > - 2D structure display > - More documentation, screencasts, & tutorials. > - Browser plugins > - Direct MPEG movie export > - Direct WinAVI movie export > - Structure cleanup & energy minimization > - Objects/states split over multiple windows (side by side views) > - Multi-line text annotations in scenes > - APBS bundled witih PyMOL > - Per-object Z clip > - "native" Windows user interface in a single window > - Undo > - Improved molecular builder > - Better RigiMOL integration > - MOPAC integration > - Sequence alignment editing > - 3D PDF export > - Cleaned up matrix & transformation interface > - Blender integration > - Nucleic acid building > - Calculate surface areas and volumes > - Secondary structure display in sequence viewer > - Scene buttons / sorter > - Movie "slider" ala Cinema4D/Maya/3DSMax > - Drag & drop programming of object motions > > or > > Pymol MMTK integration? > > > Best, > Anders > > > > > > > > Cheers, > > Warren > > > > > > > > > -----Original Message----- > > > From: pymol-users-boun...@lists.sourceforge.net > > > [mailto:pymol-users-boun...@lists.sourceforge.net] On > Behalf > Of > > Anders Norgaard > Sent: Wednesday, March 05, 2008 8:53 AM > To: > > pymol-users@lists.sourceforge.net > Subject: [PyMOL] Will Pymol > > participate in Google Summer of Code 2008? > > > > > > Hi, > > > > > > > > > I guess that it is one of the great ways to catch young new > > > contributors. > > > > > > http://code.google.com/soc/2008/ > > > > > > > > > Best, > > > Anders > > > > > > -------------------------------------------------------------- > > > ----------- > > > This SF.net email is sponsored by: Microsoft Defy all > > > challenges. Microsoft(R) Visual Studio 2008. > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyMOL-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
