Radius of gyration - Revision history

Cchem: 1 revision

2019-05-28T02:27:26Z

1 revision

Speleo3: psico

2019-05-24T13:48:53Z

psico

Cchem: 1 revision

2018-04-03T18:09:06Z

1 revision

Speleo3: python3

2018-03-12T08:52:43Z

python3

Bell: 5 revisions

2014-03-28T03:53:01Z

5 revisions

Speleo3: example

2011-04-01T07:53:15Z

example

Speleo3 at 18:58, 31 March 2011

2011-03-31T18:58:45Z

Speleo3: example

2011-03-31T18:56:56Z

example

Speleo3: categories

2011-03-31T18:34:56Z

Speleo3: page created

2011-03-31T18:31:24Z

page created

New page

This script does calcualate the [http://en.wikipedia.org/wiki/Radius_of_gyration radius of gyration] of a molecule.

Thanks to Tsjerk Wassenaar for posting this script on the [http://sourceforge.net/mailarchive/message.php?msg_id=27288491 pymol-users mailing list]!

<source lang="python">
from pymol import cmd
from itertools import izip
import math

def rgyrate(selection='(all)', quiet=1):
'''
DESCRIPTION

Radius of gyration

USAGE

rgyrate [ selection ]
'''
quiet = int(quiet)
model = cmd.get_model(selection).atom
x = [i.coord for i in model]
mass = [i.get_mass() for i in model]
xm = [(m*i,m*j,m*k) for (i,j,k),m in izip(x,mass)]
tmass = sum(mass)
rr = sum(mi*i+mj*j+mk*k for (i,j,k),(mi,mj,mk) in izip(x,xm))
mm = sum((sum(i)/tmass)**2 for i in izip(*xm))
rg = math.sqrt(rr/tmass - mm)
if not quiet:
print "Radius of gyration: %.2f" % (rg)
return rg

cmd.extend("rgyrate", rgyrate)

# vi:expandtab
</source>

@@ Line 1: / Line 1: @@
 This script does calcualate the [http://en.wikipedia.org/wiki/Radius_of_gyration radius of gyration] of a molecule.
 Thanks to Tsjerk Wassenaar for posting this script on the [http://sourceforge.net/mailarchive/message.php?msg_id=27288491 pymol-users mailing list]!
 <source lang="python">
@@ Line 63: / Line 69: @@
 === See Also ===
-[[Center Of Mass]], [[COM]]
+* [[centerofmass]]
 [[Category:Script_Library]]
 [[Category:Math_Scripts]]

@@ Line 52: / Line 52: @@
 cmd.show('cartoon', 'chain A')
-stored.gyradius = radiusOfGyration.rgyrate('chain A and polymer')
+r = radiusOfGyration.rgyrate('chain A and polymer')
-centerOfMass.com('chain A and polymer', object='com')
+centerOfMass.com('chain A and polymer', object='com', vdw=r)
 util.cbc()

@@ Line 40: / Line 40: @@
 [[File:Radius_of_gyration_Example.png|300px|thumb|right]]
-This example used the radius of gyration and the [[Center_Of_Mass|center of mass]] to display a semitransparent sphere.
+This example uses the radius of gyration and the [[Center_Of_Mass|center of mass]] to display a semitransparent sphere.
 <source lang="python">
 from pymol import cmd, stored, util
-import centerOfMass, rgyrate
+import centerOfMass, radiusOfGyration
 cmd.set('sphere_transparency', 0.5)
@@ Line 52: / Line 52: @@
 cmd.show('cartoon', 'chain A')
-stored.gyradius = rgyrate.rgyrate('chain A and polymer')
+stored.gyradius = radiusOfGyration.rgyrate('chain A and polymer')
 centerOfMass.com('chain A and polymer', object='com')
 cmd.alter('last com', 'vdw=stored.gyradius')

← Older revision		Revision as of 18:56, 31 March 2011
Line 34:		Line 34:

	# vi:expandtab		# vi:expandtab
		+	</source>
		+
		+	=== Example ===
		+
		+	[[File:Radius_of_gyration_Example.png\|300px\|thumb\|right]]
		+
		+	This example used the radius of gyration and the [[Center_Of_Mass\|center of mass]] to display a semitransparent sphere.
		+
		+	<source lang="python">
		+	from pymol import cmd, stored, util
		+	import centerOfMass, rgyrate
		+
		+	cmd.set('sphere_transparency', 0.5)
		+
		+	cmd.fetch('2xwu')
		+	cmd.hide('everything')
		+	cmd.show('cartoon', 'chain A')
		+
		+	stored.gyradius = rgyrate.rgyrate('chain A and polymer')
		+	centerOfMass.com('chain A and polymer', object='com')
		+	cmd.alter('last com', 'vdw=stored.gyradius')
		+
		+	util.cbc()
	</source>		</source>

← Older revision		Revision as of 18:34, 31 March 2011
Line 35:		Line 35:
	# vi:expandtab		# vi:expandtab
	</source>		</source>
		+
		+	=== See Also ===
		+
		+	[[Center Of Mass]], [[COM]]
		+
		+	[[Category:Script_Library]]
		+	[[Category:Math_Scripts]]

← Older revision	Revision as of 02:27, 28 May 2019
(No difference)

← Older revision	Revision as of 18:09, 3 April 2018
(No difference)

@@ Line 5: / Line 5: @@
 <source lang="python">
 from pymol import cmd
 import math
@@ Line 18: / Line 17: @@
      rgyrate [ selection ]
      '''
      quiet = int(quiet)
      model = cmd.get_model(selection).atom
@@ Line 28: / Line 31: @@
      rg = math.sqrt(rr/tmass - mm)
      if not quiet:
-         print "Radius of gyration: %.2f" % (rg)
+         print("Radius of gyration: %.2f" % (rg))
      return rg

← Older revision	Revision as of 03:53, 28 March 2014
(No difference)