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> 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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>
>
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--
Tsjerk A. Wassenaar, Ph.D.
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