Tsjerk,
Can you add an example of generating a “real” membrane around a protein to the
gallery of the PyMOLwiki?
My students would love to have easy access to that!
Thanks!
Adam
> On Feb 2, 2016, at 1:39 AM, Tsjerk Wassenaar <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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