Re: [PyMOL] How to get pymol 1.4
Hi Jason, many thanks for your reply and efforts. I hope you have a good time at the meetings. Keep up the good work !! cheers, Abhi On Wed, Mar 23, 2011 at 8:06 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Stephen, I would like to know if, and when, 1.4 will be available for downloading. Yes, PyMOL v1.4 will be released to the open-source. I will prepare the v1.4 release file soon (hopefully less than two weeks' time). As Michael noted, it's nothing insidious: within hours of releasing the v1.4 to the incentive users, I had to get in a plane and fly to the west coast to present and support PyMOL. I'm at the crystallographic WCPCW meeting this week, and ACS next week. When I return home, I'll merge the volumes code and make the release file. I'll announce it when I finish and it's posted. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
Re: [PyMOL] How to get pymol 1.4
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.eswrote: 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
Re: [PyMOL] How to get pymol 1.4
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
Re: [PyMOL] How to get pymol 1.4
Thanks for pointing out Jason's email. I missed that. And at the same time I shall learn to read and understand the fine-print under open source. On Wed, Mar 23, 2011 at 12:12 PM, 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 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___ http://p.sf.net/sfu/intel-dev2devmar___ PyMOL-users mailing list ( PyMOL-users@lists.sourceforge.net PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 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 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 https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 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
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 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___ http://p.sf.net/sfu/intel-dev2devmar___ PyMOL-users mailing list ( PyMOL-users@lists.sourceforge.net PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users https://lists.sourceforge.net/lists/listinfo/pymol-users Archives:
Re: [PyMOL] How to get pymol 1.4
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
Re: [PyMOL] How to get pymol 1.4
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
Re: [PyMOL] How to get pymol 1.4
Hi Stephen, I would like to know if, and when, 1.4 will be available for downloading. Yes, PyMOL v1.4 will be released to the open-source. I will prepare the v1.4 release file soon (hopefully less than two weeks' time). As Michael noted, it's nothing insidious: within hours of releasing the v1.4 to the incentive users, I had to get in a plane and fly to the west coast to present and support PyMOL. I'm at the crystallographic WCPCW meeting this week, and ACS next week. When I return home, I'll merge the volumes code and make the release file. I'll announce it when I finish and it's posted. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
Re: [PyMOL] How to get pymol 1.4
Thank you for your reply. I was too much in a hurry to write. I shall curb my impatience and wait for your announcement. Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivriate http://www.FoundationForChemistry.com -Original Message- From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Sent: Wednesday, March 23, 2011 3:07 PM To: Stephen P Molnar Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to get pymol 1.4 Hi Stephen, I would like to know if, and when, 1.4 will be available for downloading. Yes, PyMOL v1.4 will be released to the open-source. I will prepare the v1.4 release file soon (hopefully less than two weeks' time). As Michael noted, it's nothing insidious: within hours of releasing the v1.4 to the incentive users, I had to get in a plane and fly to the west coast to present and support PyMOL. I'm at the crystallographic WCPCW meeting this week, and ACS next week. When I return home, I'll merge the volumes code and make the release file. I'll announce it when I finish and it's posted. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
