Difference between revisions of "Get Area"

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===USAGE===
 
===USAGE===
 
<source lang="python">
 
<source lang="python">
get_area sele [,state ]
+
get_area sele [,state[, load_b ]]
 
</source>
 
</source>
  
 
===PYMOL API===
 
===PYMOL API===
 
<source lang="python">
 
<source lang="python">
cmd.get_area(string selection="(all)", state=0 )
+
cmd.get_area(string selection="(all)", load_b=0, state=0 )
 
</source>
 
</source>
  
 
= Example =
 
= Example =
'''Ref: Warren Dalano, PyMol Users List'''.
 
 
 
<source lang="python">
 
<source lang="python">
 
# load components separately
 
# load components separately
Line 44: Line 42:
 
print complex_area
 
print complex_area
 
print (ligand_area + target_area) - complex_area
 
print (ligand_area + target_area) - complex_area
 +
</source>
 +
 +
<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>
 
</source>
  
 
== See Also ==
 
== See Also ==
[[Surface]], most notably [[Surface#Calculating_a_partial_surface]].
+
* For an example of '''load_b''' in use check out [[FindSurfaceResidues]].
 +
* [[Surface]], most notably [[Surface#Calculating_a_partial_surface]].
  
 
[[Category:Commands|Get Area]]
 
[[Category:Commands|Get Area]]
 
[[Category:Biochemical_Properties|Get Area]]
 
[[Category:Biochemical_Properties|Get Area]]

Revision as of 09:15, 4 November 2009

get_area calculates the surface area in square Angstroms of the selection given.

USAGE

get_area sele [,state[, load_b ]]

PYMOL API

cmd.get_area(string selection="(all)", load_b=0, state=0 )

Example

# 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 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

See Also