In addition to David's excellent email, I would like to point out that Jason is extremely dedicated to the open-source future of PyMOL, so much so that I don't think a better PyMOL maintainer could have been chosen. 

I think that, for people who have been using/contributing to PyMOL for a long time, there's a natural inclination to say "Oh no! A more commercial entity is now in charge!" and assume that things are both worse than they are and likely to get even worse. I certainly had some of those thoughts myself, but I've talked with Jason many times (sometimes initiated by me and sometimes initiated by him) and I'm convinced that things are in excellent hands.

Just as an example of how it's easy to assume the worst, there have been quite a few complaints about the way in which PyMOL is hosted on Sourceforge. People went to download the source and, instead of a source tarball, found a link to a text file. Outrage at the fact that the actual source had somehow been hidden was then expressed. First of all, that text file contained very clear instructions on how to actually download the source. Second, and this will likely come as a complete shock to the people who complained, the text file is EXACTLY the system that Warren put in place. You may want to read that again, because, as far as I know, nobody complained about the system when Warren was in charge, but many people lept to the conclusion that nefarious forces were at work when they saw the exact same system under Schrodinger. Third, and perhaps most important, Jason's reaction upon hearing these complaints was to add a source tarball to the Sourceforge download page. If you go to pymol.org and click on "open source", you go directly to the Sourceforge page from which you can download that tarball. So, if anything, PyMOL's open-source nature is *more* accessible now.

I would say the the creation of the Warren L. DeLano Memorial PyMOL Open-Source Fellowship also clearly demonstrates Schrodinger's commitment to both open source and the PyMOL community, although I should mention in the interest of full disclosure that I have the great honor of receiving the 2010-2011 fellowship.

I'm sure there are several other examples like this, but the main thing I'd like to say is that Jason is very accessible (both via email and through this list) and extremely responsive. If you're worried about something, especially something as important as the continuing open-source nature of PyMOL, try sending a collegial email to the list. PyMOL's userbase is huge, and I'm sure that many other people have the same concern. I'm also sure that Jason (or someone else on the list) will give you a surprisingly good answer. Open-source code thrives on community and trust, and I've really seen no signs to indicate that those aren't still to be had in top-notch form with PyMOL.

Cheers,

-Michael

On Wed, Mar 23, 2011 at 7:12 AM, <lists@cowsandmilk.net> wrote:
a) you're mistaken, Warren's incentive builds had extra features.  Also, Warren had announced pretty clear plans of adding more features to the incentive builds and not releasing them open source for several years
b) if you've been following the list, Jason has stated that many of the 1.4 features are on their way to the open source repository.

Sure, I am of the type that wishes all features were open source and that Jason did all development directly against a repository we could all see, but I think he's done a good job communicating the way development is happening to the list and schrodinger's model for the incentive builds seems to be hardly different from what Warren had started doing.

-David

On Mar 23, 2011, at 6:33 AM, Abhinav Verma <abhinav1205@gmail.com> wrote:

And why would that be? I thought that pymol is open source and till Warren was there all updates were available in the open source domain and incentive builds were limited to windows executable and involving support!!




On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij <mjvanraaij@cnb.csic.es> wrote:
> Is the 1.4 version restricted to incentive downloads only??

Yes

>
> Thanks,
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