Get Area - Revision history

Cchem: 1 revision

2021-12-06T03:43:03Z

1 revision

Speleo3: Speleo3 moved page Get Area to Get area: lower case spelling

2021-11-23T22:12:19Z

Speleo3 moved page Get Area to Get area: lower case spelling

Cchem: 1 revision

2020-07-20T16:19:41Z

1 revision

Speleo3: flag ignore in PyMOL 2.5

2020-06-23T06:48:32Z

flag ignore in PyMOL 2.5

Cchem: 1 revision

2020-06-22T05:01:41Z

1 revision

Speleo3: dot_hydrogens

2020-06-16T13:35:00Z

dot_hydrogens

Cchem: 1 revision

2018-07-25T05:40:11Z

1 revision

Speleo3: usage/arguments

2018-06-20T14:54:56Z

usage/arguments

Bell: 1 revision

2015-10-19T01:22:01Z

1 revision

OsvaldoMartin: add example of using a Python script to compute the SASA for individual residues

2015-08-26T23:51:28Z

add example of using a Python script to compute the SASA for individual residues

← Older revision		Revision as of 22:12, 23 November 2021
Line 1:		Line 1:
−	'''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.	+	#REDIRECT [[Get 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.
−
−	~~'''Attention:''' Atoms with the "[[Surface~~#~~Calculating_a_partial_surface\|ignore]]"~~ [[~~flag]] may lead to unexpected results. Clear the "ignore" flag first or exclude those atoms from the calculation.~~
−	''Fixed in PyMOL 2.5, [https://github.com/schrodinger/pymol-open-source/commit/1659fde83d2a125f86cad13414cead6b8f74abe9 ignored atoms are now excluded]. Previously, their entire sphere surface was added to the surface area.''
−
−	~~= Usage =~~
−
−	~~get_area [ selection [, state [, load_b ]]]~~
−
−	~~== Arguments ==~~
−
−	* '''selection''' = str: atom selection {default: all}
−	* '''state''' = int: object state {default: 1}
−	* '''load_b''' = 0/1: Load the surface area per atom into the b-factor {default: 0}
−
−	~~== Settings ==~~
−
−	~~The following PyMOL settings control how '''get_area''' works:~~
−
−	~~{\| class="wikitable"~~
−	\|-
−	~~! Setting~~
−	~~! Description~~
−	\|-
−	~~\| [[dot_solvent]]~~
−	~~\| '''0''' = calculate '''molecular surface'''~~ area ~~{default}~~
−	~~'''1''' = calculate '''solvent accessible surface''' area (SASA)~~
−	\|-
−	~~\| [[dot_density]]~~
−	~~\| 1-4 {default: 2}. Sampling density. Higher density (more dots) means higher accuracy but slower performance.~~
−	\|-
−	~~\| [[solvent_radius]]~~
−	~~\| The solvent radius {default: 1.4}~~
−	\|}
−
−	~~The [[dot_hydrogens]] setting is '''not''' used.~~
−
−	~~For example:~~
−	~~<source lang="python">~~
−	~~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.~~
−	~~</source>~~
−
−	~~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.~~
−
−	~~== Python API ==~~
−	~~<source lang="python">~~
−	~~float cmd.get_area(str selection="(all)", int state=1, int load_b=0)~~
−	~~</source>~~
−
−	~~= Examples =~~
−	~~== Example 1 - starting with a complex in a single file ==~~
−	~~<source lang="python">~~
−	~~# 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~~
−	~~</source>~~
−
−	~~== Example 2 - starting with two components in separate files ==~~
−	~~<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>~~
−
−	~~==Example 3 - using load_b to get surface area per atom ==~~
−	~~<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>~~
−
−
−	~~==Example 4 - using a Python script to compute the SASA for individual residues==~~
−	~~<source lang="python">~~
−	~~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~~
−	~~</source>~~
−
−
−	~~= See Also =~~
−	* For an example of '''load_b''' in use check out [[FindSurfaceResidues]].
−	* [[Surface]], most notably [[Surface#Calculating_a_partial_surface]].
−
−	~~[[Category:Commands\|Get Area]]~~
−	~~[[Category:Biochemical_Properties\|Get Area~~]]

@@ Line 3: / Line 3: @@
 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.
-'''Attention:''' Atoms with the "[[Surface#Calculating_a_partial_surface|ignore]]" [[flag]] may lead to unexpected results (their entire sphere surface is counted instead of their molecular surface contribution). Clear the "ignore" flag first or exclude those atoms from the calculation.
+'''Attention:''' Atoms with the "[[Surface#Calculating_a_partial_surface|ignore]]" [[flag]] may lead to unexpected results. Clear the "ignore" flag first or exclude those atoms from the calculation.
 = Usage =

@@ Line 34: / Line 34: @@
 | The solvent radius {default: 1.4}
 |}
 For example:

@@ Line 1: / Line 1: @@
 '''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 "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:
-'''[[dot_solvent]]'''
+{| class="wikitable"
-:: '''0''' = calculate '''molecular surface''' area
+|-
-:: '''1''' = calculate '''solvent accessible surface''' area (SASA)
+! Setting
 For example:
 <source lang="python">
@@ Line 36: / Line 56: @@
 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.
-===USAGE===
+== Python API ==
 <source lang="python">
-cmd.get_area(string selection="(all)", load_b=0, state=0 )
+float cmd.get_area(str selection="(all)", int state=1, int load_b=0)
 </source>

@@ Line 7: / Line 7: @@
 '''[[dot_solvent]]'''
 :: '''0''' = calculate '''molecular surface''' area
-:: '''1''' = calculate '''solvent accessible surface''' area
+:: '''1''' = calculate '''solvent accessible surface''' area (SASA)
 '''[[dot_density]]'''
@@ Line 127: / Line 127: @@
 </source>
-== See Also ==
 * For an example of '''load_b''' in use check out [[FindSurfaceResidues]].
 * [[Surface]], most notably [[Surface#Calculating_a_partial_surface]].

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