read Jasons mail: Greetings,
I'm delighted to announce that the Incentive build of PyMOL v1.4 has been released. Current subscribers can download the binaries for Windows, Mac and Linux from http://pymol.org/dsc/ip and access documentation and videos from http://pymol.org/dsc/dokuwiki/doku.php?id=media:new14. As you will see, the PyMOL builds are much larger. This is because we're shipping a newer and much fuller version of Python, optimized libraries for map generation, and chemistry libraries for the new stereochemical labeling and atom typing. Here's the Incentive PyMOL v1.4 feature list: • New 64-bit MacPyMOL allows Mac users to access more than 4 GB of memory • Volume visualization for unique display of volumetric data and simultaneous visualization of multiple iso-surfaces (see http://pymol.org/volume) • Electron density map generation from reflection data (Mac and Linux only, Windows coming soon) • Stereochemical labeling • Improved Atom Typing; SYBYL/MOL2 and MacroModel support • OpenGL Shaders (GLSL) for improved on-screen rendering (cartoons, sticks, surfaces, volumes). • Dynamic measurements (distances, bond angles and dihedral angles) • File > Save Molecule now allows saving of multiple files, multi-state PDBs to a single file, and multi-state PDBs to multiple files • Improved State Handling makes operations on multi-state objects easier • Built using updated and Schrödinger-compatible distribution of Python (v2.7). • PyMOL Web GUI (PWG) • Several bug fixes Many of these features are already in the open-source code. Within the next few weeks, we will put the volume visualization and shaders into the open-source code. Stereochemical labeling and map generation are not in the open-source project, but we are working on adding them to the open-source project. I will send an update soon when the volume visualization is in the open-source code. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net On 23 Mar 2011, at 19:50, Stephen P Molnar wrote: > Going to www.pymol.org, clicking on OpenSource and then > sf.net/projects/pymol/develop followed by Download PyMOL Molecular Graphics > System will download pumol-1.3r2-src.tar.bz2. > > I would like to know if, and when, 1.4 will be available for downloading. > > Stephen P. Molnar, Ph.D. Life is a > fuzzy set > Foundation for Chemistry Stochastic > and multivriate > http://www.FoundationForChemistry.com > > From: Michael Lerner [mailto:mgler...@gmail.com] > Sent: Wednesday, March 23, 2011 2:22 PM > To: li...@cowsandmilk.net > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] How to get pymol 1.4 > > 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, <li...@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 <abhinav1...@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 <mjvanra...@cnb.csic.es> > wrote: > > Is the 1.4 version restricted to incentive downloads only?? > > Yes > > > > > Thanks, > > ------------------------------------------------------------------------------ > > Enable your software for Intel(R) Active Management Technology to meet the > > growing manageability and security demands of your customers. Businesses > > are taking advantage of Intel(R) vPro (TM) technology - will your software > > be a part of the solution? Download the Intel(R) Manageability Checker > > today! > > http://p.sf.net/sfu/intel-dev2devmar_______________________________________________ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > ------------------------------------------------------------------------------ > Enable your software for Intel(R) Active Management Technology to meet the > growing manageability and security demands of your customers. Businesses > are taking advantage of Intel(R) vPro (TM) technology - will your software > be a part of the solution? Download the Intel(R) Manageability Checker > today! http://p.sf.net/sfu/intel-dev2devmar > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > ------------------------------------------------------------------------------ > Enable your software for Intel(R) Active Management Technology to meet the > growing manageability and security demands of your customers. Businesses > are taking advantage of Intel(R) vPro (TM) technology - will your software > be a part of the solution? Download the Intel(R) Manageability Checker > today! http://p.sf.net/sfu/intel-dev2devmar > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > -- > Michael Lerner, Ph.D. > IRTA Postdoctoral Fellow > Laboratory of Computational Biology NIH/NHLBI > 5635 Fishers Lane, Room T909, MSC 9314 > Rockville, MD 20852 (UPS/FedEx/Reality) > Bethesda MD 20892-9314 (USPS) > ------------------------------------------------------------------------------ > Enable your software for Intel(R) Active Management Technology to meet the > growing manageability and security demands of your customers. Businesses > are taking advantage of Intel(R) vPro (TM) technology - will your software > be a part of the solution? Download the Intel(R) Manageability Checker > today! > http://p.sf.net/sfu/intel-dev2devmar_______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
