Dear Nicolas, As for the semi-transparent sphere, there are a number of ways to do that. One option: You could create a new object named new_obj with an atom at the center point and use "alter new_obj, vdw=radius" to make the sphere. Then use "set sphere_transparency, 0.5, new_obj"
Alternatively, you could make a cgo object: http://pymolwiki.org/index.php/Ellipsoid Now, on to your first question: If you use the first approach I mention for making your sphere, then this problem is also solved because now you have an atom to select around. Cheers, Mike Z On Tue, May 18, 2010 at 11:22 PM, Nicolas Bock <nicolasb...@gmail.com>wrote: > Hello, > > I would like to do the following: I have a large protein loaded in pymol. I > would like to select all atoms within a radius around a point. I know about > "select within", however, this command requires the second selection to be > an atom. I would prefer if the center of the sphere is not necessarily > centered on an atom. Is this possible? In addition I would like to draw the > spherical selection region somewhat transparently, so that I can illustrate > what I have selected. Is that possible? > > Thanks already, > > nick > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > 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 Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University
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