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 wrote:
>
> Hi all,
>
> about proteins inserted into membranes, the group of M
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 co
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 g
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 downl
Thanks Jared, this worked.
Since I only have the extracellular domains of the receptors, i used the
center-of-mass of all extracellular domains as one point,
and the centre-of-mass of the alpha atoms closest to the membrane for all
receptor moleculees as a second point,
then shifted copies of
Hi all,
translate does seem to work with CGOs if you use named arguments (note the
'object=' in the argument list):
cmd.translate([x,y,z], object='membrane')
Here's an example that you can copy and paste into pymol:
---
python
from pymol.cgo import *
from pymol import cmd
from pymol.vf
Hi Annemarie -
Fun problem. It looks like cmd.transform_selection() only works with
"molecule" type objects, not with CGOs. You could try doing something like
what's in the 3rd example in http://www.pymolwiki.org/index.php/Axes,
calculating the new object matrix itself by transforming the curr
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 genera
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 t
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 relati
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
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