Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

[vincent Chaptal]

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/

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 > 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" 
> 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 > 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
> 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
> 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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[PyMOL] status of Uppsala EDS server?

[Robert Hanson]

Does anyone know the status of http://eds.bmc.uu.se? Is it gone forever?
Does anyone know the replacement URL for getting electron density maps and
difference maps?  (Which I think is at EBI, right?)

Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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