Difference between revisions of "Radius of gyration"

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{{Infobox psico
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|module    =  psico.querying#gyradius
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}}
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This script does calcualate the [http://en.wikipedia.org/wiki/Radius_of_gyration radius of gyration] of a molecule.
 
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]!
 
Thanks to Tsjerk Wassenaar for posting this script on the [http://sourceforge.net/mailarchive/message.php?msg_id=27288491 pymol-users mailing list]!
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 +
''The function was added to [[psico]] as "gyradius".''
  
 
<source lang="python">
 
<source lang="python">
 
from pymol import cmd
 
from pymol import cmd
from itertools import izip
 
 
import math
 
import math
  
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     rgyrate [ selection ]
 
     rgyrate [ selection ]
 
     '''
 
     '''
 +
    try:
 +
        from itertools import izip
 +
    except ImportError:
 +
        izip = zip
 
     quiet = int(quiet)
 
     quiet = int(quiet)
 
     model = cmd.get_model(selection).atom
 
     model = cmd.get_model(selection).atom
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     rg = math.sqrt(rr/tmass - mm)
 
     rg = math.sqrt(rr/tmass - mm)
 
     if not quiet:
 
     if not quiet:
         print "Radius of gyration: %.2f" % (rg)
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         print("Radius of gyration: %.2f" % (rg))
 
     return rg
 
     return rg
  
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cmd.show('cartoon', 'chain A')
 
cmd.show('cartoon', 'chain A')
  
stored.gyradius = radiusOfGyration.rgyrate('chain A and polymer')
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r = radiusOfGyration.rgyrate('chain A and polymer')
centerOfMass.com('chain A and polymer', object='com')
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centerOfMass.com('chain A and polymer', object='com', vdw=r)
cmd.alter('last com', 'vdw=stored.gyradius')
 
  
 
util.cbc()
 
util.cbc()
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=== See Also ===
 
=== See Also ===
  
[[Center Of Mass]], [[COM]]
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* [[centerofmass]]
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* [[Center Of Mass]]
 +
* [[COM]]
  
 
[[Category:Script_Library]]
 
[[Category:Script_Library]]
 
[[Category:Math_Scripts]]
 
[[Category:Math_Scripts]]

Latest revision as of 08:48, 24 May 2019

Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.querying#gyradius

This script does calcualate the radius of gyration of a molecule.

Thanks to Tsjerk Wassenaar for posting this script on the pymol-users mailing list!

The function was added to psico as "gyradius".

from pymol import cmd
import math

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

    Radius of gyration

USAGE

    rgyrate [ selection ]
    '''
    try:
        from itertools import izip
    except ImportError:
        izip = zip
    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

Example

Radius of gyration Example.png

This example uses the radius of gyration and the center of mass to display a semitransparent sphere.

from pymol import cmd, stored, util
import centerOfMass, radiusOfGyration

cmd.set('sphere_transparency', 0.5)

cmd.fetch('2xwu')
cmd.hide('everything')
cmd.show('cartoon', 'chain A')

r = radiusOfGyration.rgyrate('chain A and polymer')
centerOfMass.com('chain A and polymer', object='com', vdw=r)

util.cbc()

See Also