On Feb 2, 2016, at 1:39 AM, Tsjerk Wassenaar <tsje...@gmail.com
<mailto:tsje...@gmail.com>> wrote:
Hi Annemarie,
It's actually quite simple to generate a real membrane around
your protein and, e.g., to show the head groups. Do you have a
PDB ID for the protein, or are they in-house models?
Cheers,
Tsjerk
On Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich
<jul...@joules.de <mailto:jul...@joules.de>> wrote:
Hi Annemarie,
Have you tried the following?
cmd.translate([x,y,z], object='membrane')
replace x,y,z with your translation vector.
Cheers,
Julian
On Sat, Jan 30, 2016 at 8:33 AM, 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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Tsjerk A. Wassenaar, Ph.D.
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