Hi Roger,
Unfortunately, there is no CGO ellipsoid. What you might try is
represent the units in the lattice as arrows as to indicate their
orientation (determined as the principal or principle ;) axis), and have
one unit in (cartoon) detail, with a more slender arrow inside. I think
it would give enough idea to the viewer of how the thing is packed :)
Hope it helps,
Tsjerk
You can create an arrow by using a cylinder and a set of ever smaller
spheres for the arrow tip.
Robert Campbell wrote:
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
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