On 09/12/2017 15:56, chemocev marker wrote:
I am wondering is there clear way to show these forces like H-bond. I tried
KING and can see the VDW radii but not the visual representation. Does coot has any option for this?
Coot uses the VdW radii in the Refmac monomer library.
Maybe Measures -> Environment Distances is what you want? The yellow lines are
the non-Hydrogen-bond bumps.
Or maybe coot_contact_dots_for_ligand_py is what you want? The attached script will add a menu item for you.
You can see the whole surface by activating the check-button in
Draw -> Generic Display Objects -> vdw-surface
Paul
def wrap_coot_contact_dots():
active_atom = active_residue()
if (not active_atom):
print "No active atom"
else:
imol = active_atom[0]
chain_id = active_atom[1]
res_no = active_atom[2]
ins_code = active_atom[3]
atom_name = active_atom[4]
alt_conf = active_atom[5]
coot_contact_dots_for_ligand_py(imol, [chain_id, res_no, ins_code])
if have_coot_python:
if coot_python.main_menubar():
menu = coot_menubar_menu("VdW")
if menu:
add_simple_coot_menu_menuitem(menu, "Coot Isolated Dots",
lambda func: wrap_coot_contact_dots())
