Difference between revisions of "Get Area"

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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.
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===USAGE===
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<source lang="python">
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get_area sele [,state ]
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</source>
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===PYMOL API===
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<source lang="python">
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cmd.get_area(string selection="(all)", state=0 )
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</source>
  
 
= Example =
 
= Example =
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[[Surface]], most notably [[Surface#Calculating_a_partial_surface]].
 
[[Surface]], most notably [[Surface#Calculating_a_partial_surface]].
  
[[Category:Commands|get area]]
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[[Category:Commands|Get Area]]
[[Category:Biochemical_Properties]]
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[[Category:Biochemical_Properties|Get Area]]

Revision as of 09:57, 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.