Thank you both for your kind help.
I will follow this up today and let you know how it goes.
-Yarrow
> Greetings,
>
> Please also investigate the following settings:
>
> # needs a real atom selection
> surface_carve_selection
>
> # distance from the above selection to cull surfaces
> surface_ca
Greetings,
Please also investigate the following settings:
# needs a real atom selection
surface_carve_selection
# distance from the above selection to cull surfaces
surface_carve_cutoff
I looked at your data and there is a small problem. You have a few points
where one atom is mapped to multip
Hi Yarrow -
If you add "br. " to the show surface command, you will get more continuous
surfaces, as the selection will be made by residue instead of by atom.
show surface, br. protein within 0.5 of pocket_selection
If you don't want to show the surface from a particular residue (e.g. if it's
Thank you for your help Thomas,
Using your settings I get a lot of "partial surfaces"
Showing the surface around the Pocket selection like this:
show surface, protein within 0.5 of pocket_selection
worked well but I still see a piece of surface that I really don't want to
show up. I guess I can
Hi Yarrow,
should be as simple as:
PyMOL> hide surface
PyMOL> show surface, (organic around 8.0)
PyMOL> set transparency, 0.3
PyMOL> set two_sided_lighting
See also:
http://pymolwiki.org/index.php/Selection_Algebra
Hope that helps.
Cheers,
Thomas
Yarrow Madrona wrote, On 03/03/13 18:34:
> H
Hello,
Does anyone know how to visualize a surface within a given radius from a
ligand binding site? In chimera you can limit the display surface within
0-X angstrom of a ligand. This allows you to see the surface surrounding
the ligand without the rest of the protein.
I guess you could create a
