Thread: [Apbs-users] problems with apbs generated surfaces/rotating/pymol
Biomolecular electrostatics software
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From: Florian S. <sch...@cr...> - 2011-07-18 22:31:17
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Dear All, I seem to be having trouble to rotate APBS generated surfaces, visualized in pymol. E.g. I used the command "rotate, y, 180, mypdb.pdb" in pymol, to rotate my molecule by 180 deg. The molecule is rotated but the surface changes appearance and does not show the potential of the solv. accessible surface it was coloured in. Has anybody else seen this too? Cheers, Florian ----------------------------------------------------------- Florian Schmitzberger, PhD Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, Seeley G. Mudd 123 Boston, MA 02115, US Tel: 001 617 432 5603 |
From: Michael L. <mgl...@gm...> - 2011-07-19 01:51:41
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Hi Florian, "Rotate" rotates just the atomic coordinates, but not the computed potential. Try "turn" to move just the camera. Cheers, -Michael On Mon, Jul 18, 2011 at 6:02 PM, Florian Schmitzberger < sch...@cr...> wrote: > Dear All, > > I seem to be having trouble to rotate APBS generated surfaces, > visualized in pymol. E.g. I used the command "rotate, y, 180, > mypdb.pdb" in pymol, to rotate my molecule by 180 deg. The molecule is > rotated but the surface changes appearance and does not show the > potential of the solv. accessible surface it was coloured in. > > Has anybody else seen this too? > > Cheers, > > Florian > > ----------------------------------------------------------- > Florian Schmitzberger, PhD > Biological Chemistry and Molecular Pharmacology > Harvard Medical School > 250 Longwood Avenue, Seeley G. Mudd 123 > Boston, MA 02115, US > Tel: 001 617 432 5603 > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > Storage Efficiency Calculator > This modeling tool is based on patent-pending intellectual property that > has been used successfully in hundreds of IBM storage optimization engage- > ments, worldwide. Store less, Store more with what you own, Move data to > the right place. Try It Now! > http://www.accelacomm.com/jaw/sfnl/114/51427378/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) as of August 15th: Department of Physics and Astronomy Earlham College 801 National Road West Richmond, IN 47374-4095 |
From: Florian S. <sch...@cr...> - 2011-07-19 11:49:02
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Thanks. Yes, turn works. Cheers, Florian On Jul 18, 2011, at 9:51 PM, Michael Lerner wrote: > Hi Florian, > > "Rotate" rotates just the atomic coordinates, but not the computed > potential. Try "turn" to move just the camera. > > Cheers, > > -Michael > > On Mon, Jul 18, 2011 at 6:02 PM, Florian Schmitzberger <sch...@cr... > > wrote: > Dear All, > > I seem to be having trouble to rotate APBS generated surfaces, > visualized in pymol. E.g. I used the command "rotate, y, 180, > mypdb.pdb" in pymol, to rotate my molecule by 180 deg. The molecule is > rotated but the surface changes appearance and does not show the > potential of the solv. accessible surface it was coloured in. > > Has anybody else seen this too? > > Cheers, > > Florian > > ----------------------------------------------------------- > Florian Schmitzberger, PhD > Biological Chemistry and Molecular Pharmacology > Harvard Medical School > 250 Longwood Avenue, Seeley G. Mudd 123 > Boston, MA 02115, US > Tel: 001 617 432 5603 > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > Storage Efficiency Calculator > This modeling tool is based on patent-pending intellectual property > that > has been used successfully in hundreds of IBM storage optimization > engage- > ments, worldwide. Store less, Store more with what you own, Move > data to > the right place. Try It Now! http://www.accelacomm.com/jaw/sfnl/114/51427378/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > -- > Michael Lerner, Ph.D. > IRTA Postdoctoral Fellow > Laboratory of Computational Biology NIH/NHLBI > 5635 Fishers Lane, Room T909, MSC 9314 > Rockville, MD 20852 (UPS/FedEx/Reality) > Bethesda MD 20892-9314 (USPS) > > as of August 15th: > > Department of Physics and Astronomy > Earlham College > 801 National Road West > Richmond, IN 47374-4095 > |
From: Baker, N. <Nat...@pn...> - 2011-07-19 15:13:20
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Thanks, Michael! __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://kdi.pnl.gov/bios/baker.stm From: Michael Lerner [mailto:mgl...@gm...] Sent: Monday, July 18, 2011 6:51 PM To: Florian Schmitzberger Cc: apb...@li... Subject: Re: [Apbs-users] problems with apbs generated surfaces/rotating/pymol Hi Florian, "Rotate" rotates just the atomic coordinates, but not the computed potential. Try "turn" to move just the camera. Cheers, -Michael On Mon, Jul 18, 2011 at 6:02 PM, Florian Schmitzberger <sch...@cr...<mailto:sch...@cr...>> wrote: Dear All, I seem to be having trouble to rotate APBS generated surfaces, visualized in pymol. E.g. I used the command "rotate, y, 180, mypdb.pdb" in pymol, to rotate my molecule by 180 deg. The molecule is rotated but the surface changes appearance and does not show the potential of the solv. accessible surface it was coloured in. Has anybody else seen this too? Cheers, Florian ----------------------------------------------------------- Florian Schmitzberger, PhD Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, Seeley G. Mudd 123 Boston, MA 02115, US Tel: 001 617 432 5603<tel:617%20432%205603> ------------------------------------------------------------------------------ Storage Efficiency Calculator This modeling tool is based on patent-pending intellectual property that has been used successfully in hundreds of IBM storage optimization engage- ments, worldwide. Store less, Store more with what you own, Move data to the right place. Try It Now! http://www.accelacomm.com/jaw/sfnl/114/51427378/ _______________________________________________ apbs-users mailing list apb...@li...<mailto:apb...@li...> https://lists.sourceforge.net/lists/listinfo/apbs-users -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) as of August 15th: Department of Physics and Astronomy Earlham College 801 National Road West Richmond, IN 47374-4095 |