[Chimera-users] radius of gyration

[Eric Pettersen]

Hi Marek,
	I think you're right.  I've attached an amended script that computes  
the center of mass and the mass-weighted radius of gyration.

--Eric

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On Feb 15, 2012, at 2:09 PM, Marek Maly wrote:

> Hello,
>
> Isn't it radius of gyration (molecular) related rather to center of  
> mass (gravity)
> of given molecule than to it's center of geometry ?
>
>   Best wishes,
>
>        Marek
>
>
>
>
> Dne Wed, 15 Feb 2012 21:05:24 +0100 Eric Pettersen  
> <pett at cgl.ucsf.edu> napsal/-a:
>
>> On Feb 14, 2012, at 6:07 PM, Daniel Gurnon wrote:
>>
>>> Hi Eric,
>>> The radius of gyration interest stems from a little project I'm
>>> starting with an undergrad. I'm interested in the radius of gyration
>>> because I'm curious about how accurate our pictures of biomolecules
>>> are, at least the ones that come from crystal structures. I'd like
>>> to compare predictions of size-related behavior derived from the pdb
>>> with measurements of size in solution, using gel filtration, SAXS,
>>> or light scattering. That said, I don't know if I want center of
>>> geometry or principal axis!  Any advice?
>>
>> Hi Dan,
>> 	I'm no expert, but it sounds like you want the radius of gyration
>> from the center of geometry.  Nonetheless, I'm cc'ing this to the
>> chimera-users in case any others have thoughts.
>> 	In an old posting to chimera-users, Elaine Meng provided a Fortran
>> program to compute the radius of gyration:
>>
>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003648.html
>>
>> I've attached a Python script that will print the center of geometry
>> and radius of gyration from that center in Chimera's reply log.  Run
>> the script simply by opening it with File->Open.  Depending on  
>> whether
>> you feel nearby waters and ions will contribute to the measurements
>> you are trying to model, you may or may not want to delete water and
>> ions before running the script.
>>
>> --Eric
>>
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>>                         http://www.cgl.ucsf.edu
>>
>>
>>
>>
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>
>
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