Editing Get area (section)

= Examples =
== Example 1 - starting with a complex in a single file ==
<source lang="python">
# load complex
# Haemoglobin in this example illustrates careful use of selection algebra
load 2HHB.pdb

# create objects for alpha1, beta1 and alpha1,beta1 pair of subunits
create alpha1, 2HHB and chain A
create beta1, 2HHB and chain B
create ab1, 2HHB and chain A+B

# get hydrogens onto everything (NOTE: must have valid valences on e.g. small organic molecules)
h_add

# make sure all atoms including HETATM within an object occlude one another, but ignore solvent
flag ignore, none
flag ignore, solvent

# use solvent-accessible surface with high sampling density
set dot_solvent, 1
set dot_density, 3

# measure the components individually storing the results for later
alpha1_area=cmd.get_area("alpha1")
beta1_area=cmd.get_area("beta1")


# measure the alpha1,beta1 pair
ab1_area=cmd.get_area("ab1")

# now print results and do some maths to get the buried surface
print alpha1_area
print beta1_area
print ab1_area
print (alpha1_area + beta1_area) - ab1_area
</source>

== Example 2 - starting with two components in separate files ==
<source lang="python">
# 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 including HETATM within an object occlude one another but ignore solvent
flag ignore, none
flag ignore, solvent

# 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
</source>

==Example 3 - using load_b to get surface area per atom ==
<source lang="python">
# example usage of load_b
# select some organic small molecule
select ligand, br. first organic
# get its area and load it into it's b-factor column
get_area ligand, load_b=1
# print out the b-factor/areas per atom
iterate ligand, print b
</source>


==Example 4 - using a Python script to compute the SASA for individual residues==
<source lang="python">
import __main__
__main__.pymol_argv = ['pymol','-qc']
import pymol
from pymol import cmd, stored
pymol.finish_launching()

cmd.set('dot_solvent', 1)
cmd.set('dot_density', 3)

cmd.load('file.pdb')  # use the name of your pdb file
stored.residues = []
cmd.iterate('name ca', 'stored.residues.append(resi)')

sasa_per_residue = []
for i in stored.residues:
    sasa_per_residue.append(cmd.get_area('resi %s' % i))

print sum(sasa_per_residue)
print cmd.get_area('all')  # just to check that the sum of sasa per residue equals the total area
</source>