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Re: [PyMOL] Caver 3.0 pugin
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From: Stephen P. M. <s.m...@sb...> - 2013-11-18 16:13:24
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On 11/17/2013 03:02 PM, James Starlight wrote: > Hi Stephen, > > you should try lattest CAVER which could be downloaded from > http://www.caver.cz > > before installing it via Pymol plugin menu, you should to open > caver-3.0-1.py <http://caver-3.0-1.py> and find here > CAVER3_LOCATION = "directory/where/caver3/is/located" > > and modify this on your path providing it to the jar file directly ( > in this version there is no jar path in pymol plugin itself). > > Does anyone use it for the analysis of the ligand sites? I've test it > with the GPCR and found 3 possible pathways. I'n not sure how It have > been clustered but now I'n looking for the method for the steered MD > along caver-predicted pathes > > James > > > 2013/11/17 Stephen P. Molnar <s.m...@sb... > <mailto:s.m...@sb...>> > > I would be interested in just how the problem has been solved! > > I just installed caver v-2.1.2 in the 64 bit Debian Testing with > PyMOL v-1.6.0.0 compiled from the latest svn and functioning > perfectly on my system. > > Carver installed from the PyMOL wicki via the PyMOL Plugin Manager > without any complaints. Yet when I try to use the plugin I get: > > ERROR: Directory incorrectly specified -plugin.jar not found, > check directory/where/jar/with/plugin/is/locate/Carver2_1.jar > > Both Carver2_1_2.py and Carver2_1_2.pyc are in the startup > subdirectory. Also other plugins are working without complaint. > > This is exactly the way the plug was working the last time that I > attempted its installation and use. > > > On 11/15/2013 03:14 PM, James Starlight wrote: >> This issue have been solved. Caver works fine. Does anyone tried >> to include path information obtained by caver to the NAMD steered >> md simulation? I'm looking for the protocol for guiding namd >> forces along the direction obtaned from CAVER. >> >> >> James >> >> >> 2013/11/15 James Starlight <jms...@gm... >> <mailto:jms...@gm...>> >> >> Dear Pymol Users! >> >> >> In the latest 3.0 releases of the CAVER plugin lack the >> source path for the caver.jar launch file. Could you tell me >> how I could define this path manually from pymol shell? I've >> try to make calculations with thus plugin having Caver 3.0 >> dir in the work folder but obtained error that /where/caver3 >> not found >> >> >> Thanks for help >> >> James >> >> >> >> >> ------------------------------------------------------------------------------ >> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps >> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access >> Free app hosting. Or install the open source package on any LAMP server. >> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! >> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk >> >> >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>) >> Info Page:https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives:http://www.mail-archive.com/pym...@li... > > -- > Stephen P. Molnar, Ph.D. Life is a fuzzy set > Foundation for Chemistry Stochastic and multivariate > www.FoundationForChemistry.com <http://www.FoundationForChemistry.com> > (614)312-7528 (c) > Skype: smolnar1 > > > ------------------------------------------------------------------------------ > DreamFactory - Open Source REST & JSON Services for HTML5 & Native > Apps > OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access > Free app hosting. Or install the open source package on any LAMP > server. > Sign up and see examples for AngularJS, jQuery, Sencha Touch and > Native! > http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk > _______________________________________________ > PyMOL-users mailing list (PyM...@li... > <mailto:PyM...@li...>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/pym...@li... > > Got it! Many thanks. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 |
