> On 02 Feb 2016, at 08:39, 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
>
>
Hi Tsjerk
Thanks for your suggestion,
I had of course thought about depicting a real membrane, but rejected it. The
problem is that I am dealing with very large and complex system:
Multimeric receptors crosslinked by rigid antibody-like molecules, therefore I
would require a 250Å by 250Å patch of membrane.
I would prefer a very simple representation of the membrane, not only because
of rendering times when making a movie and highly resolved images,
but also to not distract the viewer from the essential feature of the model by
extraneous detail - I just need to indicate the plane of the membrane
to show that some of the arrangements are not possible due to clashes with the
plane of the membrane.
If there is no way define my cgo object in screen coordinates or to object
transformations to it, I will either have to export the
transformed coordinates of my objects, then re-import them in the correct
orientation, or else find a reproducible way to calculate the preferred
position and orientation of my cgo object relative to my molecular objects to
generate it in the right place.
It’s just a bit tedious to do this more or less by trial and error, since I
have to do it reproducibly for a fairly large number of different arrangements.
>
> On Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich <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
Dear Julian
Neither “translate” nor “rotate” seem to work on cgo objects.
PyMOL>translate [-50,0,0], membrane
Selector-Error: Invalid selection name "membrane".
membrane<--
e.g if I indicate a helix axis with an arrow using the “AngleBetweenHelices”
script,
I have to use “turn” rather than “rotate” to get a second view rotated by 90
degree.
I suspect that cgo objects are fixed in object space, you can only alter the
camera position
to look at them from different angles.
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 Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich <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>
> 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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