Anders & Others, Just FYI: On behalf of the PyMOL Open-Source Project, DeLano Scientific yesterday applied as a mentoring organization for the Google Summer of Code 2008. Google will publish the list of accepted organizations within a week -- we'll see what happens!
In the meantime, the required GSoC "ideas" page on the Wiki has been updated with a fairly comprehensive set of ideas, many of them arising from discussions here and from the recent survey. http://www.pymolwiki.org/index.php/Gsoc2008 Whether or not GSoC happens for PyMOL the year, we should definitely plan on morphing that page into a general ideas page for the project. Please don't be afraid to add your pet idea or request to that page as well (if it isn't already covered)! Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info > -----Original Message----- > From: Anders Norgaard [mailto:anders.norga...@gmail.com] > Sent: Sunday, March 09, 2008 9:43 AM > To: DeLano Scientific > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Will Pymol participate in Google Summer > of Code 2008? > > On Fri, Mar 7, 2008 at 11:04 PM, DeLano Scientific > <del...@delsci.info> wrote: > > 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: > > Ok. I made a Wiki-page for this > > http://www.pymolwiki.org/index.php/Gsoc2008 > > And added a couple of more ideas. > > Best regards, > Anders > > > > > > > > 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 > > > > > > > > > > > >
