Hi, You can draw a CGO circle in the yz plane using:
x1,y1,z1 = -0.1, 0, 0 # start point r1,g1,b1 = 1,0,0 # color (red) x2,y2,z2 = 0.1, 0, 0 # end point r2,g2,b2 = 1,1,0 # color (yellow) radius = 10 cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], "cylinder1" ) To make it transparent, change it to cmd.load_cgo( [ 25.0, 0.25, 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], "cylinder1" ) The 9.0 stands for CYLINDER, but you'd need to 'from pymol.cgo import *' to be able to use the keywords. Likewise, 25.0 stands for ALPHA, controlling the transparency. Note that the cylinder may not look quite round. It will do when you raytrace it. I couldn't find a setting for cgo display quality... Anyway, it may be that Micheals suggestion is better, but since the question was for a cylinder... And with a bit of Python scripting such a circle could be drawn with a given center and normal axis. Hope it helps, Tsjerk On Tue, Jul 7, 2009 at 12:54 AM, Michael Lerner<mglerner+sourcefo...@gmail.com> wrote: > I'm sure there's a way to actually draw a circle, but for your particular > use it might be better to use a sphere. If you're comfortable with python > scripting, you can use CGO objects. If not, you might do something like > this: > > fetch 1hhp > create thing, resi 24 and name ca # create a new object from some single > atom selection > alter thing, vdw=10.0 # set desired radius > rebuild # necessary if spheres have already been shown > show spheres, thing > alter_state 1, thing, x,y,z = 50,60,10 # set desired x,y,z coords > set sphere_transparency, 0.5, thing # make it transparent > zoom > ray > > you can also use something like select + within to select all residues > within a cutoff, but I got the impression you wanted a nice visualization. > > > Hope that helps, > > -michael > > On Mon, Jul 6, 2009 at 5:01 PM, Benjamin Michael Owen <owe...@marshall.edu> > wrote: >> >> Does anyone know how to draw a circle with a given radius in pymol? I have >> a distance that I want to use to see what residues lie on the end of that >> radius, but I have no idea how to write the command to draw the circle. >> Could someone help me please? >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > > > > -- > 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) > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ------------------------------------------------------------------------------ Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/blackberry _______________________________________________ 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
