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'''get_area''' calculates the surface area in square Angstroms of the selection given. | '''get_area''' calculates the surface area in square Angstroms of the selection given. | ||
| + | |||
| + | ===USAGE=== | ||
| + | <source lang="python"> | ||
| + | get_area sele [,state ] | ||
| + | </source> | ||
| + | |||
| + | ===PYMOL API=== | ||
| + | <source lang="python"> | ||
| + | cmd.get_area(string selection="(all)", state=0 ) | ||
| + | </source> | ||
= Example = | = Example = | ||
| Line 39: | Line 49: | ||
[[Surface]], most notably [[Surface#Calculating_a_partial_surface]]. | [[Surface]], most notably [[Surface#Calculating_a_partial_surface]]. | ||
| − | [[Category:Commands| | + | [[Category:Commands|Get Area]] |
| − | [[Category:Biochemical_Properties]] | + | [[Category:Biochemical_Properties|Get Area]] |
Revision as of 13:57, 20 June 2009
get_area calculates the surface area in square Angstroms of the selection given.
USAGE
get_area sele [,state ]
PYMOL API
cmd.get_area(string selection="(all)", state=0 )
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
See Also
Surface, most notably Surface#Calculating_a_partial_surface.