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'''get_area''' calculates the surface area in square Angstroms of the selection given.
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#REDIRECT [[Get area]]
 
 
===USAGE===
 
<source lang="python">
 
get_area sele [,state ]
 
</source>
 
 
 
===PYMOL API===
 
<source lang="python">
 
cmd.get_area(string selection="(all)", state=0 )
 
</source>
 
 
 
= Example =
 
'''Ref: Warren Dalano, PyMol Users List'''.
 
 
 
<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 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
 
</source>
 
 
 
== See Also ==
 
[[Surface]], most notably [[Surface#Calculating_a_partial_surface]].
 
 
 
[[Category:Commands|Get Area]]
 
[[Category:Biochemical_Properties|Get Area]]
 

Latest revision as of 03:43, 6 December 2021

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