Hi Annemarie -
Fun problem. It looks like cmd.transform_selection() only works with
"molecule" type objects, not with CGOs. You could try doing something like
what's in the 3rd example in http://www.pymolwiki.org/index.php/Axes,
calculating the new object matrix itself by transforming the current one, then
applying it to the object using cmd.set_object_ttt().
Alternatively, if you can reproducibly identify any vector that should be
perpendicular to the membrane, you could use those points as the start and end
points for your initial load_cgo command. For example, if your receptor
happens to have a symmetric channel, something like this might work.
```
# create pseudoatoms at the average positions of residues at the top and bottom
of the chain
pseudoatom top, <some_residue_at_top_of_channel> and n. CA and chain A+B+C+D
pseudoatom bot, <some_residue_at_bottom_of_channel> and n. CA and chain A+B+C+D
# Orient to the pseudoatoms and fine tune the positions along the viewport Y
axis.
# (Make sure you don't move the view until you're done positioning the
pseudoatoms.)
orient (top or bot)
turn z, 90 # assuming `orient` put them along X and you want them along Y
translate [0, 2, 0], top
translate [0, -1.5, 0], bot
# Get the coordinates of the two end points
from pymol import stored
stored.start = []
stored.end = []
iterate_state 1, top, stored.start = (x,y,z)
iterate_state 1, bot, stored.end = (x,y,z)
# Create the CGO cylinder (I made it semitransparent)
from pymol.cgo import ALPHA, CYLINDER
x1,y1,z1 = stored.start
x2,y2,z2 = stored.end
r1,g1,b1 = 1, 1, 0
r2,g2,b2 = 1, 1, 0
radius = 100
cmd.load_cgo([ ALPHA, 0.5, CYLINDER, x1, y1, z1, x2, y2, z2, radius, r1, g1,
b1, r2, g2, b2 ], "membrane")
```
Not sure if that will be applicable to your use case, but hopefully it will at
least give you an idea of one approach that could work.
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Columbia University
On Jan 29, 2016, at 4:33 PM, Honegger Annemarie
<honeg...@bioc.uzh.ch<mailto:honeg...@bioc.uzh.ch>> 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
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