get_area calculates the surface area in square Angstroms of the selection given. Note that the accessibility is assessed in the context of the object(s) that the selection is part of. So, to get the surface areas of e.g. a component of a complex, you should make a new object containing a copy of just that component and calculate its area.
The "get_area selection" command will return the effective surface area of the dots that you would see from "show dots, selection". This is a discrete approximation -- not an exact calculation.
The following PyMOL settings control how get_area works:
- 0 = calculate molecular surface area
- 1 = calculate solvent accessible surface area (SASA)
- The accuracy of the measurement depends on the density of dots, which is controlled by the "dot_density" setting (1-4).
- The solvent radius is controlled by the "solvent_radius" setting (default 1.4).
PyMOL> load $TUT/1hpv.pdb PyMOL> show dots, resn arg PyMOL> get_area resn arg cmd.get_area: 1147.956 Angstroms^2. PyMOL>set dot_solvent, on PyMOL>get_area resn arg cmd.get_area: 673.084 Angstroms^2. PyMOL>set dot_density, 3 PyMOL>get_area resn arg cmd.get_area: 674.157 Angstroms^2. PyMOL>set dot_density, 4 PyMOL>get_area resn arg cmd.get_area: 672.056 Angstroms^2. PyMOL>get_area all cmd.get_area: 13837.804 Angstroms^2.
This code has not been recently validated though it was checked a couple years back. We suggest that people perform some kind of independent check on their system before trusting the results.
- 1 USAGE
- 2 PYMOL API
- 3 Examples
- 4 See Also
get_area sele [,state[, load_b ]]
cmd.get_area(string selection="(all)", load_b=0, state=0 )
Example 1 - starting with a complex in a single file
# 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 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 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
Example 2 - starting with two components in separate files
# 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
Example 3 - using load_b to get surface area per atom
# 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
Example 4 - using a Python script to compute the SASA for individual residues
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