Thank you Tsjerk. What we do right now is just open VMD and use the membrane
builder, then take that file back into PyMOL!
> On Feb 3, 2016, at 12:29 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
>
> Hi Adam,
>
> Well, for putting it on the Pymol wiki, I'll at least have to wait and see
> how far my students got with integrating the routine in a webservice. If they
> already managed, it will be as easy as submitting the structure and saying
> what membrane you want. Otherwise, it will require some downloads and
> installs to get the proper programs in place, before it becomes as simple as
> running a single command specifying the protein and membrane.
>
> If you and your students would like to try it out, I can give some pointers
> and provide my scripts to get it done. The wiki will have to wait a bit, but
> it will come.
>
> Cheers,
>
> Tsjerk
>
> On Feb 2, 2016 5:33 PM, "H. Adam Steinberg" <h.adam.steinb...@gmail.com
> <mailto:h.adam.steinb...@gmail.com>> wrote:
> 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
>> <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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> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366 <tel:608%2F592-2366>
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
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