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
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@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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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 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@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
__________ Informace od ESET NOD32 Antivirus, verze databaze 6887 (20120215) __________
Tuto zpravu proveril ESET NOD32 Antivirus.
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Eric Pettersen -
Marek Maly