WOW! what a great resource! I downloaded an example and played with it in
PyMOL. They removed the Chains, making selections a little harder, but still a
great resource!
> On Feb 4, 2016, at 5:26 AM, vincent Chaptal <vincent.chap...@ibcp.fr> wrote:
>
> Hi all,
>
> about proteins inserted into membranes, the group of Mark Sansom just
> published a paper where they describe insertion of the whole
> membrane-proteins PDB into a bilayer followed by coarse-grain MD and all atom
> MD, and make the results available to everyone. It would be great if they
> could make it into a server where we submit our pdb.
>
> http://sbcb.bioch.ox.ac.uk/memprotmd/beta/
> <http://sbcb.bioch.ox.ac.uk/memprotmd/beta/>
>
> Stansfeld, P. J., et al. (2015). "MemProtMD: Automated Insertion of Membrane
> Protein Structures into Explicit Lipid Membranes." Structure.
>
>
> vincent
>
>
> On 03/02/2016 19:33, H. Adam Steinberg wrote:
>> 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
>>> <mailto: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 <
>>>> <mailto:tsje...@gmail.com>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 <
>>>> <mailto:jul...@joules.de>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 <
>>>> <mailto:honeg...@bioc.uzh.ch>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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> --
> Vincent Chaptal, PhD
> Institut de Biologie et Chimie des Protéines
> Drug Resistance and Membrane Proteins Laboratory
> 7 passage du Vercors
> 69007 LYON
> FRANCE
> +33 4 37 65 29 01
> http://www.ibcp.fr <http://www.ibcp.fr/>
>
>
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
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