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Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15
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From: H. A. S. <h.a...@gm...> - 2016-02-03 18:33:36
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Thank you Tsjerk. What we do right now is just open VMD and use the membrane builder, then take that file back into PyMOL! > On Feb 3, 2016, at 12:29 PM, Tsjerk Wassenaar <ts...@gm...> wrote: > > Hi Adam, > > Well, for putting it on the Pymol wiki, I'll at least have to wait and see how far my students got with integrating the routine in a webservice. If they already managed, it will be as easy as submitting the structure and saying what membrane you want. Otherwise, it will require some downloads and installs to get the proper programs in place, before it becomes as simple as running a single command specifying the protein and membrane. > > If you and your students would like to try it out, I can give some pointers and provide my scripts to get it done. The wiki will have to wait a bit, but it will come. > > Cheers, > > Tsjerk > > On Feb 2, 2016 5:33 PM, "H. Adam Steinberg" <h.a...@gm... <mailto:h.a...@gm...>> wrote: > Tsjerk, > > Can you add an example of generating a “real” membrane around a protein to the gallery of the PyMOLwiki? > > My students would love to have easy access to that! > > Thanks! > > Adam > >> On Feb 2, 2016, at 1:39 AM, Tsjerk Wassenaar <ts...@gm... <mailto:ts...@gm...>> wrote: >> >> Hi Annemarie, >> >> It's actually quite simple to generate a real membrane around your protein and, e.g., to show the head groups. Do you have a PDB ID for the protein, or are they in-house models? >> >> Cheers, >> >> Tsjerk >> >> On Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich <ju...@jo... <mailto:ju...@jo...>> wrote: >> Hi Annemarie, >> >> Have you tried the following? >> cmd.translate([x,y,z], object='membrane') >> >> replace x,y,z with your translation vector. >> >> Cheers, >> Julian >> >> On Sat, Jan 30, 2016 at 8:33 AM, Honegger Annemarie <hon...@bi... <mailto:hon...@bi...>> wrote: >> I am trying to show some cell surface receptors and to indicate their position relative to the membrane. >> >> I thought to indicate the plane of the membrane by a flat disk, a ago cylinder. >> >> x1,y1,z1 = 0, -1, 0 # start point >> r1,g1,b1 = 1, 1, 0 # color (yellow) >> x2,y2,z2 = 0, -2, 0 # end point >> r2,g2,b2 = 1, 1, 0 # color (yellow) >> radius = 100 >> cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], "membrane" ) >> >> When I try to move this cylinder into the correct position with cmd.transform_selection, >> using the transformation parameters extracted from get_view (reordering them as needed) >> I get the error message "Selector-Error: Invalid selection name “membrane” “ >> >> The same transform command works fine if I apply it to a pseudo atom originally generated with coordinates 0,0,0. >> >> Any suggestion how else I could indicate the membrane, or how I could place my ego object parallel >> to the screen yz plane? I have to be able to do this in a reproducible fashion, as I have to do this >> for a large number of constructs that bend my receptors relative to the membrane in various ways. >> >> Thanks for your help >> Annemarie >> >> _______________________________ >> >> Dr. Annemarie Honegger PhD >> Department >> of Biochemistry >> Zürich University >> Winterthurerstrasse 190 >> CH-8057 Zürich >> Switzerland >> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 <http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140> >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <https://lists.sourceforge.net/lists/listinfo/pymol-users> >> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...> >> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 <http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140> >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <https://lists.sourceforge.net/lists/listinfo/pymol-users> >> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...> >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________ <http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________> >> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <https://lists.sourceforge.net/lists/listinfo/pymol-users> >> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...> > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 <tel:608%2F592-2366> H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |