Comments on: What will become of PyMOL?

By: Vinod

Vinod — Mon, 09 Aug 2010 04:15:54 +0000

Dear All,

I want to know the way to generate electron density map for a small molecule. Please provide me list of free softwares? Any suggestions will be highly appreciated.

Thank you very much in advance.

Please write me to my e-mail ID rajurajpatel_1411.at.yahoo.co.in

By: Egon Willighagen

Egon Willighagen — Fri, 15 Jan 2010 07:43:17 +0000

@Joerg: indeed, free-as-in-beer is orthogonal to free-as-in-free-speech and free-as-in-opensource.

@David: I’m happy with BSD. Noel pointed me to the commits too… that is great news, and congratulation to Schrödinger for this move!

By: David Hall

David Hall — Thu, 14 Jan 2010 21:23:40 +0000

@Egon , looking at the SVN log ( http://pymol.svn.sourceforge.net/viewvc/pymol/?view=log ) for revisions 3882-3886 shows the copyright changes, etc. It also suggests acquisition of the trademark. There is essentially no change in the license or policy for using the trademark, which is good or bad depending on your feelings about BSD-like licenses.

By: Joerg Kurt Wegner

Joerg Kurt Wegner — Thu, 14 Jan 2010 20:20:31 +0000

I know Schrodinger as a company with a lot of passion for science and a very high scientific profile. Besides, they are a fantastic business partner with an excellent support (like other molecular modeling companies). There are two key commercial companies supporting KNIME (open source): one is Schrodinger, the other is the ChemicalComputingGroup. This is quite a commitment and a clear open source supportive statement. Having said this, I am very confident that they take the further development of PyMol serious. PyMol had already a dual license model: free for academics and a commercial version for industry partners. I hope this (or close version of it) will continue in the future …
Finally, I think we all agree that open source avoids reinventing the wheel, but ‘open source’ must not mean ‘for free’. Sure, there should be a low barrier for everyone getting started for contributing and integrating tools (if you do not want to do all by yourself). Nonetheless, do I have no problem with paying for getting access to more tools or unlocking some special features. And I totally agree with Tony that I would not mind seeing X percent of the money made, flowing into the direction of Warren’s family and a general life science informatics fund. This would definitely add a ‘social’ touch to the whole deal and I this is not ‘just’ any open source project, this is Warrens PyMol and always will be Warrens Pymol … keep the spirit …

By: ChemSpiderman

ChemSpiderman — Thu, 14 Jan 2010 15:36:28 +0000

I am very happy to read about Schrodinger picking up PyMol…makes TOTAL sense to me based on their working relationship to date. I had expressed concern on Friendfeed previously about what would happen to support his wife. I commented “I realize I might get slapped for this but with light comes shadow (very Jungian I know). The upside of Warren releasing code as Open Source is that his work can live on and be continued. This is brilliant. The shadow is what about about his young wife that he has left behind? I talked with Warren earlier this year and PyMol was helping him to create a living. But what does his family get from his work now he is gone? I thought of similar things when ChemSPider was developed. I hope that some organization will take his code under their wing, keep it Open Source and support it, but be honorable enough to divert some of the funds to his wife for all of the long nights she likely didn’t see him while he was coding a fix for someone. He was working on it for almost a decade or so. Feel free to poke at me…but I needed to say it based on my discussions with him a few months ago…”
I hope that Warren’s estate has been appropriately compensated for his passion, commitment and contribution to science. He earned it.

By: Egon Willighagen

Egon Willighagen — Thu, 14 Jan 2010 14:43:02 +0000

I am curious about the exact details of the agreement… but most interested in knowing about the fine prints around the copyrights… have Warren’s copyright been reassigned to Schrödinger in this deal?

If Schrödinger can live up to the promise to support the Open Source community around PyMol by keeping the source GPL (or make it have a even a more liberal license) and sell prebuild binaries (as the past business model was, right?), that would make a interesting development… not so many commercial parties active in the Open Source bio/cheminformatics community…

Really interesting news!

By: David Hall

David Hall — Wed, 13 Jan 2010 17:52:23 +0000

The fact that they’ve hired Jason to me is an encouraging sign. He has put a lot of work into the pymolwiki, without which the open documentation for pymol would be much smaller. See for instance, Pymol Movie School http://www.pymolwiki.org/index.php/MovieSchool

Also, from Jason’s time at BU (with Simon Kasif), he seemed fairly committed to the idea of open source for a lot of software, in those cases where our conversation drifted that way. Usually we just talked science, which was the reason he would come to visit our lab.

I actually think this could present some new opportunities. We’re seeing commits again to the svn repository, coming from multiple committers. (before it was only ever delano, even if the code came from someone else) and http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/data/pymol/splash.png?revision=3887&view=markup is a lot kinder splash page for open source users than http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/data/pymol/splash.old.png?revision=3570&view=markup