Re: [PyMOL] Super, algorithm
I would also be interested if there is any documentation about the super algorithm and the differences to align. -Spencer On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin aloctavo...@gmail.com wrote: Hi, Exactly which algorithm is behind the super command? How the outliers pairs are defined? The is some scientific paper related to super or it is really an experimental idea? Thanks. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111iu=/4140/ostg.clktrk ___ 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 -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751iu=/4140/ostg.clktrk___ 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] Super, algorithm
Hi Spencer, unfortunately, to our knowledge, no formal documentation for the super align method exists. It's a sequence-independant (means: residue name independent) sequence alignment method based on 3D coordinates of CA atoms. The RMSD minimizing superposition with outlier rejection is identical to the align command. Cheers, Thomas On 26 Nov 2014, at 07:13, Spencer Bliven sbli...@ucsd.edu wrote: I would also be interested if there is any documentation about the super algorithm and the differences to align. -Spencer On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin aloctavo...@gmail.com wrote: Hi, Exactly which algorithm is behind the super command? How the outliers pairs are defined? The is some scientific paper related to super or it is really an experimental idea? Thanks. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751iu=/4140/ostg.clktrk ___ 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] Super, algorithm
Hi Spencer - If you need a superposition algorithm with a published reference, try CEAlignhttp://www.pymolwiki.org/index.php/Cealign. Some references are listed on the page for the former CEAlign Pluginhttp://www.pymolwiki.org/index.php/Cealign_plugin#References from before it was incorporated into PyMOL (in version 1.3). Just be careful to note that the order of the first two arguments (target, mobile) is switched compared to the `super` and `align` commands (mobile, target). Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Nov 26, 2014, at 7:13 AM, Spencer Bliven sbli...@ucsd.edumailto:sbli...@ucsd.edu wrote: I would also be interested if there is any documentation about the super algorithm and the differences to align. -Spencer On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin aloctavo...@gmail.commailto:aloctavo...@gmail.com wrote: Hi, Exactly which algorithm is behind the super command? How the outliers pairs are defined? The is some scientific paper related to super or it is really an experimental idea? Thanks. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751iu=/4140/ostg.clktrk___ 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 -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751iu=/4140/ostg.clktrk___ 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] Super, algorithm
Hi Spencer, If you are interested I have implemented a (preliminary version) of a superposition algorithm (similar to super) using Python/PyMOL. Cheers, Osvaldo. On Wed, Nov 26, 2014 at 2:40 PM, Sampson, Jared jared.samp...@nyumc.org wrote: Hi Spencer - If you need a superposition algorithm with a published reference, try CEAlign http://www.pymolwiki.org/index.php/Cealign. Some references are listed on the page for the former CEAlign Plugin http://www.pymolwiki.org/index.php/Cealign_plugin#References from before it was incorporated into PyMOL (in version 1.3). Just be careful to note that the order of the first two arguments (target, mobile) is switched compared to the `super` and `align` commands (mobile, target). Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Nov 26, 2014, at 7:13 AM, Spencer Bliven sbli...@ucsd.edu wrote: I would also be interested if there is any documentation about the super algorithm and the differences to align. -Spencer On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin aloctavo...@gmail.com wrote: Hi, Exactly which algorithm is behind the super command? How the outliers pairs are defined? The is some scientific paper related to super or it is really an experimental idea? Thanks. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111iu=/4140/ostg.clktrk ___ 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 -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751iu=/4140/ostg.clktrk___ 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 -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751iu=/4140/ostg.clktrk___ 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
[PyMOL] Super, algorithm
Hi, Exactly which algorithm is behind the super command? How the outliers pairs are defined? The is some scientific paper related to super or it is really an experimental idea? Thanks. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111iu=/4140/ostg.clktrk___ 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
