Joel,
Yes, PyMOL does have this capability, but it is immature and not
routinely validated.
The basic concepts are:
1) get_area selection command will return the effective surface area
of the dots that you would see from show dots, selection. This is a
discrete approximation -- not an exact
Close, but it depends on whether you want the surface area of the
residues alone, or in the context of the molecule.
load protein.pdb
get_area resn arg
will be less than
create arg_object, resn arg
get_area arg_object
This is because the first example will give you only the exposed area
Hi Warren,
I found out that it is possible to write out AMBER style atom name
formats with hydrogens added using the Chempy which is pretty neat.
However it seems like this does not recognize the N-terminal residue
for adding hydrogens. Is that still the case? I am still using PyMOL
088 (I
