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'''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.
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#REDIRECT [[Get area]]
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===USAGE===
 
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<source lang="python">
 
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get_area sele [,state[, load_b ]]
 
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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)", load_b=0, state=0 )
 
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</source>
 
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= Example =
 
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<source lang="python">
 
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# load components separately
 
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load my_ligand.pdb
 
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load my_target.pdb
 
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# get hydrogens onto everything (NOTE: must have valid valences on the ligand...)
 
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h_add
 
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# make sure all atoms within an object occlude one another
 
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flag ignore, none
 
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# use solvent-accessible surface with high sampling density
 
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set dot_solvent, 1
 
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set dot_density, 3
 
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# measure the components individually
 
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ligand_area=cmd.get_area("my_ligand")
 
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target_area=cmd.get_area("my_target")
 
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# create the complex
 
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create my_complex, my_ligand my_target
 
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# measure the complex
 
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complex_area=cmd.get_area("my_complex")
 
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# now print results
 
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print ligand_area
 
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print target_area
 
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print complex_area
 
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print (ligand_area + target_area) - complex_area
 
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</source>
 
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<source lang="python">
 
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# example usage of load_b
 
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# select some organic small molecule
 
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select ligand, br. first organic
 
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# get its area and load it into it's b-factor column
 
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get_area ligand, load_b=1
 
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# print out the b-factor/areas per atom
 
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iterate ligand, print b
 
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</source>
 
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== See Also ==
 
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* For an example of '''load_b''' in use check out [[FindSurfaceResidues]].
 
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* [[Surface]], most notably [[Surface#Calculating_a_partial_surface]].
 
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[[Category:Commands|Get Area]]
 
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[[Category:Biochemical_Properties|Get Area]]
 

Latest revision as of 03:43, 6 December 2021

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