Re: [Avogadro-devel] First Avogadro 2 beta release
Hi Marcus, Really great to hear that avogadro2 is now on the scene and I'm excited to see how it develops in the future. It's already looking very impressive - I read in some pretty big molecules and the performance and responsiveness was incredibly snappy. Where's the place to log bug reports while it's still in the initial testing phase? I found one (see below) but it wasn't immediately obvious on the openchemistry website where the tracker was. Best wishes, Jens Bugs: 1. draw C atom, click Extensions - Open Babel - Add Hydrogens: Command-line output: OBProcess::executeObabel: Running /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel -icml -ocml -h /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel stderr: == *** Open Babel Error in RegisterOptionParam The number of parameters needed by option t in The LPMD file format. differs from an earlier registration. 0 molecules converted Bad CML: On 11 April 2013 19:54, Marcus D. Hanwell marcus.hanw...@kitware.comwrote: Hi, I wanted to let people on these lists know that we just made our first beta release of Avogadro 2, along with MoleQueue and MongoChem. Please see the blog post here, http://blog.cryos.org/archives/265-First-Open-Chemistry-Beta-Release.html We have created binary installers for Windows and Mac OS X, along with regular source releases, http://www.openchemistry.org/OpenChemistry/resources/software.html These are not feature complete, and we intend to make regular releases as new features land in master. There are several exciting new features, along with some missing pieces that will be brought back as we can get to them. I will work on making a screen cast highlighting how the three applications can be used together soon, and discussing some of the new features in more detail. We have automated as much of the testing and release process as possible, and will continue to streamline things. Binaries are uploaded nightly to the dashboards for Windows and Mac, and API documentation is updated nightly, http://cdash.openchemistry.org/ http://doc.openchemistry.org/avogadrolibs/api/ Avogadro 2 also uses a different binary name, and library names, meaning that there should be no problems in installing Avogadro 1 and 2 on the same system in the same prefixes. There is lots more to do before, so I will get back to it, but I hope you will check out what we have been working on. I will see if I can get some more of the features you have grown to expect back in Avogadro 2. Thanks, Marcus -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] First Avogadro 2 beta release
Hi Jens, On Fri, Apr 12, 2013 at 5:00 AM, Jens linuck...@gmail.com wrote: Really great to hear that avogadro2 is now on the scene and I'm excited to see how it develops in the future. It's already looking very impressive - I read in some pretty big molecules and the performance and responsiveness was incredibly snappy. Great to hear the positive feedback! Out of curiousity, just how big were your molecules? Where's the place to log bug reports while it's still in the initial testing phase? I found one (see below) but it wasn't immediately obvious on the openchemistry website where the tracker was. We have a bug tracker up here: http://projects.openchemistry.org/ I'll add a link on the openchemistry wiki and see about adding one to www.openchemistry.org. As for the bug: draw C atom, click Extensions - Open Babel - Add Hydrogens: Command-line output: OBProcess::executeObabel: Running /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel -icml -ocml -h /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel stderr: == *** Open Babel Error in RegisterOptionParam The number of parameters needed by option t in The LPMD file format. differs from an earlier registration. 0 molecules converted Bad CML: I noticed this odd behavior in obabel and brought it up on openbabel-devel a little while ago, see http://forums.openbabel.org/obabel-h-bug-while-adding-hydrogens-td4655976.html. This is a feature, not a bug from their perspective. We plan to implement our own add-hydrogens routine (and maybe even our own remove-hydrogens, if I can figure that out ;-) ). I've filed a bug for this here: http://projects.openchemistry.org/issues/169 Thanks for the feedback! Dave -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] First Avogadro 2 beta release
On Fri, Apr 12, 2013 at 9:29 AM, David Lonie david.lo...@kitware.com wrote: Hi Jens, On Fri, Apr 12, 2013 at 5:00 AM, Jens linuck...@gmail.com wrote: Really great to hear that avogadro2 is now on the scene and I'm excited to see how it develops in the future. It's already looking very impressive - I read in some pretty big molecules and the performance and responsiveness was incredibly snappy. Great to hear the positive feedback! Out of curiousity, just how big were your molecules? Where's the place to log bug reports while it's still in the initial testing phase? I found one (see below) but it wasn't immediately obvious on the openchemistry website where the tracker was. We have a bug tracker up here: http://projects.openchemistry.org/ I'll add a link on the openchemistry wiki and see about adding one to www.openchemistry.org. The main site already has a link (Resources, Bug Tracker), we can certainly get links on the wiki too. The Doxygen links there too, but let's work on making it as obvious as possible. As for the bug: draw C atom, click Extensions - Open Babel - Add Hydrogens: Command-line output: OBProcess::executeObabel: Running /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel -icml -ocml -h /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel stderr: == *** Open Babel Error in RegisterOptionParam The number of parameters needed by option t in The LPMD file format. differs from an earlier registration. 0 molecules converted Bad CML: I noticed this odd behavior in obabel and brought it up on openbabel-devel a little while ago, see http://forums.openbabel.org/obabel-h-bug-while-adding-hydrogens-td4655976.html. This is a feature, not a bug from their perspective. We plan to implement our own add-hydrogens routine (and maybe even our own remove-hydrogens, if I can figure that out ;-) ). I've filed a bug for this here: http://projects.openchemistry.org/issues/169 There seem to be a few bugs on the Mac with obabel and CML too, so I am afraid geometry optimization looks a little dicey. I think there are some simple workarounds we can implement there to improve things in the next release. Thanks for the feedback Jens. I think ensuring anyone can have Avogadro 1 and 2 installed should make it easier to try out the new stuff without having to give up Avogadro 1. Marcus -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] First Avogadro 2 beta release
Hi Dave and Marcus, No problem - like I said it's great to see Avogadro2 getting underway and I'm glad to be able to help. The molecule I looked at earlier was just under 9000 atoms. Avogadro 1 crashes on reading it unless I import the molecule and turn off the bond order perceiving functionality, and there is a noticeable lag when I rotate the molecule. With Avogadro2, it whizzes round instantly. Keep up the great work! Jens PS - having said that I just tried loading a pdb of a protein I'm working on (3HAP) and I just get a big yellow blob, so there may still be the odd niggle to iron out... ;) I'll file a bug report as soon as my account on the tracker is activated. On 12 April 2013 15:35, Marcus D. Hanwell marcus.hanw...@kitware.comwrote: On Fri, Apr 12, 2013 at 9:29 AM, David Lonie david.lo...@kitware.com wrote: Hi Jens, On Fri, Apr 12, 2013 at 5:00 AM, Jens linuck...@gmail.com wrote: Really great to hear that avogadro2 is now on the scene and I'm excited to see how it develops in the future. It's already looking very impressive - I read in some pretty big molecules and the performance and responsiveness was incredibly snappy. Great to hear the positive feedback! Out of curiousity, just how big were your molecules? Where's the place to log bug reports while it's still in the initial testing phase? I found one (see below) but it wasn't immediately obvious on the openchemistry website where the tracker was. We have a bug tracker up here: http://projects.openchemistry.org/ I'll add a link on the openchemistry wiki and see about adding one to www.openchemistry.org. The main site already has a link (Resources, Bug Tracker), we can certainly get links on the wiki too. The Doxygen links there too, but let's work on making it as obvious as possible. As for the bug: draw C atom, click Extensions - Open Babel - Add Hydrogens: Command-line output: OBProcess::executeObabel: Running /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel -icml -ocml -h /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel stderr: == *** Open Babel Error in RegisterOptionParam The number of parameters needed by option t in The LPMD file format. differs from an earlier registration. 0 molecules converted Bad CML: I noticed this odd behavior in obabel and brought it up on openbabel-devel a little while ago, see http://forums.openbabel.org/obabel-h-bug-while-adding-hydrogens-td4655976.html . This is a feature, not a bug from their perspective. We plan to implement our own add-hydrogens routine (and maybe even our own remove-hydrogens, if I can figure that out ;-) ). I've filed a bug for this here: http://projects.openchemistry.org/issues/169 There seem to be a few bugs on the Mac with obabel and CML too, so I am afraid geometry optimization looks a little dicey. I think there are some simple workarounds we can implement there to improve things in the next release. Thanks for the feedback Jens. I think ensuring anyone can have Avogadro 1 and 2 installed should make it easier to try out the new stuff without having to give up Avogadro 1. Marcus -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
[Avogadro-devel] First Avogadro 2 beta release
Hi, I wanted to let people on these lists know that we just made our first beta release of Avogadro 2, along with MoleQueue and MongoChem. Please see the blog post here, http://blog.cryos.org/archives/265-First-Open-Chemistry-Beta-Release.html We have created binary installers for Windows and Mac OS X, along with regular source releases, http://www.openchemistry.org/OpenChemistry/resources/software.html These are not feature complete, and we intend to make regular releases as new features land in master. There are several exciting new features, along with some missing pieces that will be brought back as we can get to them. I will work on making a screen cast highlighting how the three applications can be used together soon, and discussing some of the new features in more detail. We have automated as much of the testing and release process as possible, and will continue to streamline things. Binaries are uploaded nightly to the dashboards for Windows and Mac, and API documentation is updated nightly, http://cdash.openchemistry.org/ http://doc.openchemistry.org/avogadrolibs/api/ Avogadro 2 also uses a different binary name, and library names, meaning that there should be no problems in installing Avogadro 1 and 2 on the same system in the same prefixes. There is lots more to do before, so I will get back to it, but I hope you will check out what we have been working on. I will see if I can get some more of the features you have grown to expect back in Avogadro 2. Thanks, Marcus -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
