Dear Kanika, I do not know how to calculate the Rg using PyMOL. If it is possible, I would also like to know how. However, there are other possibilities. Do you have the pdb file of the molecule from what you want to calculate the radius of gyration? If so, you may use the program CRYSOL (download: http://www.embl-hamburg.de/biosaxs/crysol.html), which is used for comparison with SAXS data. When you run that program, you can search within the log file the parameter "Envelope Rg". But, keep in mind that the program takes into account a solvation layer of about 3 Angstroms. You can also try the HydroPro program (http://leonardo.inf.um.es/macromol/programs/hydropro/hydropro.htm), which I believe that makes the Rg calculation, but I rarely use this program for that. I am sure that HydroPro can provide you the hydrodynamic radius, but I am not sure about the Rg.
Regards, Julio De: kanika sharma [mailto:[email protected]] Enviada em: quinta-feira, 31 de março de 2011 14:46 Para: pymol-users Assunto: [PyMOL] radius of gyration After going through the script library and tutorial, I couldn't find information about calculating the radius of gyration. Is this possible in pymol? And after this I want to generate a virtual cube around it of a specific length. Thanks, Kanika
------------------------------------------------------------------------------ Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf
_______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
