Difference between revisions of "Get Area"

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m (Example)
Line 21: Line 21:
  
 
# measure the components individually
 
# measure the components individually
ligand_area=3Dcmd.get_area("my_ligand")
+
ligand_area=cmd.get_area("my_ligand")
target_area=3Dcmd.get_area("my_target")
+
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=3Dcmd.get_area("my_complex")
+
complex_area=cmd.get_area("my_complex")
  
 
# now print results
 
# now print results

Revision as of 10:26, 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