pymol-users

[PyMOL] volume approximation

[ormus c. <or...@in...>]

hi, i am looking for some advice. i would like to create a set of overlappi=
ng spheres whose combined volume approximates the=20
actual volume of a protein of interest. obviously, i am looking for a reduc=
ed representation. ideally, i am talking about no=20
more than a handful of spheres. these spheres should all be equally sized a=
nd the degree of overlap between spheres should be=20
consistent across all of them (that is, they should all overlap all neighbo=
ring spheres equally). i'm trying to construct an=20
algorithm that would take in the pdb coordinates of the protein to be appro=
ximated and output a set of points corresponding to=20
the origins of the spheres required to fill the volume of the original prot=
ein to some determined degree of accuracy (eg. >=20
90%).

i'm relatively new to pymol, but of all the molecular visualization program=
s i have looked at, it seems best suited to the=20
task at hand. has anyone done anything even remotely like this? can anyone =
offer insight as to whether i can do this within=20
pymol and, if so, where i might look (wiki, documenation, etc) to get start=
ed?

thanks in advance, ormus


--=20
India.com free e-mail - www.india.com.=20
Check out our value-added Premium features, such as an extra 20MB for mail =
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RE: [PyMOL] volume approximation

[Peter T. <pet...@bi...>]

Hi Ormus,

Not sure if this can easily be done in PyMol, but I used HydroNMR and
HydroPro for something similar for the process of analysing the =
hydrodynamic
properties of molecules. As far as I remember they don't work with
overlapping spheres but fill the space of a molecule with spheres of =
equal
size.

See Torre, Huertas and Carrasco (2000) Journal of Magnetic Resonance, =
147,
138pp

or=20

http://leonardo.fcu.um.es/macromol/programs/hydronmr/hydronmr.htm

Peter

--=20
Dr Peter Teriete
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
South Parks Rd.
Oxford
OX1 3QU
=20
Tel: +44 1865 275742
Fax: +44 1865 275182


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of ormus cama
Sent: 05 August 2005 01:04
To: pym...@li...
Subject: [PyMOL] volume approximation



hi, i am looking for some advice. i would like to create a set of
overlapping spheres whose combined volume approximates the=20
actual volume of a protein of interest. obviously, i am looking for a
reduced representation. ideally, i am talking about no=20
more than a handful of spheres. these spheres should all be equally =
sized
and the degree of overlap between spheres should be=20
consistent across all of them (that is, they should all overlap all
neighboring spheres equally). i'm trying to construct an=20
algorithm that would take in the pdb coordinates of the protein to be
approximated and output a set of points corresponding to=20
the origins of the spheres required to fill the volume of the original
protein to some determined degree of accuracy (eg. >=20
90%).

i'm relatively new to pymol, but of all the molecular visualization =
programs
i have looked at, it seems best suited to the=20
task at hand. has anyone done anything even remotely like this? can =
anyone
offer insight as to whether i can do this within=20
pymol and, if so, where i might look (wiki, documenation, etc) to get
started?

thanks in advance, ormus


--=20
India.com free e-mail - www.india.com.=20
Check out our value-added Premium features, such as an extra 20MB for =
mail
storage, POP3, e-mail forwarding, and ads-free mailboxes!


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