Hi Roger, * Roger Dodd <rb...@cam.ac.uk> [2004-10-07 16:33] wrote: > > I am trying to prepare a figure illustrating a fairly complex packing > arrangement in a large H32 (R32) unit cell, where the packing may > actually have some biological relevance. To try and show the packing > I've been generating symmetry related molecules using the symexp > command. The problem I've been running into is that things become too > complex and cluttered, whether I use lines, ribbons, cartoons, etc. My > asymmetric unit contains 2 homo-pentamers and my question is - would it > be possible to replace each monomer with, for example, an ellipsoid of > roughly the same size centred on the subunit's centre of mass to > simplify things? Is this the sort of thing that could be done with a cgo > object? Any help or other suggestions would be greatly appreciated.
You could set solvent_radius to some large number, like 5 or 10 and show the molecules' surface. The main problem is that there tend to be holes in the surface unless you set the surface_quality up to 1, in which case it can take quite a bit longer to draw. A CGO ellipsoid might be your best bet, but I'm not sure if there is a CGO ellipsoid. An approximation to the ellipsoid could be the "SAUSAGE" instead: from pymol.cgo import * from pymol import cmd # simple example obj2 = [ SAUSAGE, 0., 0., 0., 10., 0., 0., 4.0, 1.0, 1.0, 1.0, 0.5, 0.0, 0., SAUSAGE, 0., 0., 0., 0., 15., 0., 4.0, 1.0, 1.0, 1.0, 0., 0.5, 0., SAUSAGE, 0., 0., 0., 0., 0., 20., 4.0, 1.0, 1.0, 1.0, 0., 0.0, 0.5, ] cmd.load_cgo(obj2,'cyl') You would need to come up with appropriate starting and ending vertices (the first 6 numbers in each line) and the radius (the 7th number). The last 6 numbers are the starting and ending rgb colour values. I guess whether this could work would depend on how close your monomer could be approximated by a sausage. :) Cheers, Rob -- Robert L. Campbell, Ph.D. <r...@post.queensu.ca> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
