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 = | ||
| − | |||
| − | |||
<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
- For an example of load_b in use check out FindSurfaceResidues.
- Surface, most notably Surface#Calculating_a_partial_surface.