Thanks Jared, this worked.
Since I only have the extracellular domains of the receptors, i used the
center-of-mass of all extracellular domains as one point,
and the centre-of-mass of the alpha atoms closest to the membrane for all
receptor moleculees as a second point,
then shifted copies of this second pseudo atom farther down the axis to define
position and thickness of the membrane.
At least for the symmetrical assemblies this looks really good- I have to see
wether I have to find another definition for
the more skewed arrangements. Rather than having to go through extracting the
coordinates from the pseudo atoms to
use cmd.load_go, the atoms can be directly passed as parameters to the
draw_cylinder command in “draw_cylinder_cgo.py"
Thanks to everybody who helped me with their suggestions! I’ll aknowledge you
in my next seminar
best regards
Annemarie
_______________________________
Dr. Annemarie Honegger PhD
Department
of Biochemistry
Zürich University
Winterthurerstrasse 190
CH-8057 Zürich
Switzerland
e-Mail: honeg...@bioc.uzh.ch
websites
http://www.bioc.uzh.ch/plueckthun
http://www.bioc.uzh.ch/plueckthun/antibody
http://www.bioc.uzh.ch/plueckthun/nanowelt
> On 02 Feb 2016, at 20:55, Sampson, Jared M. <jms2...@cumc.columbia.edu> wrote:
>
> 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
> <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
>
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