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
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 -
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
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
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
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:
