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Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #996 - 2 msgs
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From: Michael G. L. <ml...@um...> - 2005-09-13 18:27:41
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On Tue, 13 Sep 2005, surendra negi wrote: > check this link! > http://www.csb.yale.edu/userguides/graphics/pymol/electro.html > That page is actually quite out of date. I emailed them about it a few months ago, but didn't get a response. You don't need to go through any of that hassle to use the APBS plugin these days .. it comes included with PyMOL. Yay for open source! :) -michael -- www.umich.edu/~mlerner | _ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mlerner@umich > Hope it wud help. > best sn > > --- pym...@li... wrote: > >> Send PyMOL-users mailing list submissions to >> pym...@li... >> >> To subscribe or unsubscribe via the World Wide Web, >> visit >> >> > https://lists.sourceforge.net/lists/listinfo/pymol-users >> or, via email, send a message with subject or body >> 'help' to >> pym...@li... >> >> You can reach the person managing the list at >> pym...@li... >> >> When replying, please edit your Subject line so it >> is more specific >> than "Re: Contents of PyMOL-users digest..." >> >> >> Today's Topics: >> >> 1. Displaying an electrostatic potential on msms >> (Anna Feldman-Salit) >> 2. Re: Displaying an electrostatic potential on >> msms (Peter Adrian Meyer) >> >> --__--__-- >> >> Message: 1 >> Date: Mon, 12 Sep 2005 11:25:39 +0200 >> From: Anna Feldman-Salit >> <ann...@em...> >> To: pym...@li... >> Subject: [PyMOL] Displaying an electrostatic >> potential on msms >> >> Dear All, >> >> I have a 0.98 PyMol version with APBS and >> Iso_Sliders plugins. However, >> my aim is not just visualize isosurfaces of >> electrostatic potential at >> certain values, but to display/map it on molecular >> surface. >> >> Would you be so kind to share your knowledge with me >> on this subject? >> >> I'd appreciate any help or advice of yours! >> >> Thanks, >> >> Anna. >> >> >> --__--__-- >> >> Message: 2 >> Date: Mon, 12 Sep 2005 12:03:54 -0400 (EDT) >> Subject: Re: [PyMOL] Displaying an electrostatic >> potential on msms >> From: "Peter Adrian Meyer" <pa...@co...> >> To: "Anna Feldman-Salit" >> <ann...@em...> >> Cc: pym...@li... >> >> Hi Anna, >> I generally run apbs seperately (due to difficulties >> with Alphas), but use >> the plugin to display with pymol. apbs will >> produce two output files, >> acc.dx and pot.dx. acc.dx is the electrostatic >> potential mapped to the >> solvent accessible surface; pot.dx is the >> electrostatic potential over the >> grid. What I generally do is to load acc.dx into >> pymol, and they use the >> plugin->apbs->display to show the surface (not sure >> of the exact sequence; >> pymol's doing a ray-tracing job for me at the moment >> so I can't check). >> >> Hope this helps...I've never tried the iso_sliders >> plugin. I believe the >> author of the apbs plugin is on this list, and will >> probably give you >> clearer answers. >> >> Pete >> >>> Dear All, >>> >>> I have a 0.98 PyMol version with APBS and >> Iso_Sliders plugins. However, >> my aim is not just visualize isosurfaces of >> electrostatic potential at >> certain values, but to display/map it on molecular >> surface. >>> >>> Would you be so kind to share your knowledge with >> me on this subject? >>> >>> I'd appreciate any help or advice of yours! >>> >>> Thanks, >>> >>> Anna. >>> >>> >>> >> > ------------------------------------------------------- >>> SF.Net email is Sponsored by the Better Software >> Conference & EXPO >> September 19-22, 2005 * San Francisco, CA * >> Development Lifecycle >> Practices >>> Agile & Plan-Driven Development * Managing >> Projects & Teams * Testing & >> QA >>> Security * Process Improvement & Measurement * >> http://www.sqe.com/bsce5sf >>> _______________________________________________ >>> PyMOL-users mailing list >>> PyM...@li... >>> >> > https://lists.sourceforge.net/lists/listinfo/pymol-users >>> >> >> >> Pete Meyer >> Fu Lab >> BMCB grad student >> Cornell University >> >> >> >> >> >> >> >> --__--__-- >> >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> > https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> End of PyMOL-users Digest >> > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > |