Difference between revisions of "Get area"
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# measure the components individually | # measure the components individually | ||
− | ligand_area= | + | ligand_area=cmd.get_area("my_ligand") |
− | target_area= | + | target_area=cmd.get_area("my_target") |
# create the complex | # create the complex | ||
Line 28: | Line 28: | ||
# measure the complex | # measure the complex | ||
− | complex_area= | + | complex_area=cmd.get_area("my_complex") |
# now print results | # now print results |
Revision as of 11:26, 23 April 2006
Get Area
get_area calculates the surface area in square Angstroms of the selection given.
Example
Ref: Warren Dalano, PyMol Users List.
# load components separately
load my_ligand.pdb
load my_target.pdb
# get hydrogens onto everything (NOTE: must have valid valences on the ligand...)
h_add
# make sure all atoms within an object occlude one another
flag ignore, none
# use solvent-accessible surface with high sampling density
set dot_solvent, 1
set dot_density, 3
# measure the components individually
ligand_area=cmd.get_area("my_ligand")
target_area=cmd.get_area("my_target")
# create the complex
create my_complex, my_ligand my_target
# measure the complex
complex_area=cmd.get_area("my_complex")
# now print results
print ligand_area
print target_area
print complex_area
print (ligand_area + target_area) - complex_area