From: Sara Nichols <sara.nichols@ya...>  20050524 16:34:58

Hi List, After a quick search of the list archives and the wiki, I couldn't find information about calculating the radius of gyration. Is this possible in pymol? And if it is, can you select specific residues and calculate the radius of gyration of your selection? Thanks in advance, Sara 
From: kanika sharma <ksharma997@gm...>  20110331 12:46:30
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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 
From: Julio Cesar da Silva <julio.silva@ln...>  20110331 13:19:17
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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.emblhamburg.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:ksharma997@...] Enviada em: quintafeira, 31 de março de 2011 14:46 Para: pymolusers 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 
From: Tsjerk Wassenaar <tsjerkw@gm...>  20110331 14:07:03

Hi :) The radius of gyration is not that tough. Here's a python script to do it in pymol. Do note that the hydrodynamic radius is something related, but different. from pymol import cmd import math def rgyrate(selection): # Get the atoms for the selection model=cmd.get_model(selection).atom # Extract the coordinates x=[i.coord for i in model] # Get the masses mass=[i.get_mass() for i in model] # Massweighted coordinates xm=[(m*i,m*j,m*k) for (i,j,k),m in zip(x,mass)] # Sum of masses tmass=sum(mass) # First part of the sum under the sqrt rr=sum(mi*i+mj*j+mk*k for (i,j,k),(mi,mj,mk) in zip(x,xm)) # Second part of the sum under the sqrt mm=sum((sum(i)/tmass)**2 for i in zip(*xm)) # Radius of gyration rg=math.sqrt(rr/tmassmm) # Print it... print "Radius of gyration:", rg return rg cmd.extend("rgyrate",rgyrate) Hope it helps, Tsjerk On Thu, Mar 31, 2011 at 3:03 PM, Julio Cesar da Silva <julio.silva@...> wrote: > 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.emblhamburg.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:ksharma997@...] > Enviada em: quintafeira, 31 de março de 2011 14:46 > Para: pymolusers > 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/mswebmatrixsf > > _______________________________________________ > PyMOLusers mailing list (PyMOLusers@...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymolusers > Archives: http://www.mailarchive.com/pymolusers@... >  Tsjerk A. Wassenaar, Ph.D. postdoctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands 
From: Thomas Holder <speleo3@us...>  20110331 19:02:41

Hi Tsjerk, very nice script! I have added it to the PyMOLWiki at http://pymolwiki.org/index.php/Radius_of_gyration Cheers, Thomas Tsjerk Wassenaar wrote, On 03/31/11 16:07: > Hi :) > > The radius of gyration is not that tough. Here's a python script to do > it in pymol. Do note that the hydrodynamic radius is something > related, but different. > > from pymol import cmd > import math > > def rgyrate(selection): > # Get the atoms for the selection > model=cmd.get_model(selection).atom > # Extract the coordinates > x=[i.coord for i in model] > # Get the masses > mass=[i.get_mass() for i in model] > # Massweighted coordinates > xm=[(m*i,m*j,m*k) for (i,j,k),m in zip(x,mass)] > # Sum of masses > tmass=sum(mass) > # First part of the sum under the sqrt > rr=sum(mi*i+mj*j+mk*k for (i,j,k),(mi,mj,mk) in zip(x,xm)) > # Second part of the sum under the sqrt > mm=sum((sum(i)/tmass)**2 for i in zip(*xm)) > # Radius of gyration > rg=math.sqrt(rr/tmassmm) > # Print it... > print "Radius of gyration:", rg > return rg > > cmd.extend("rgyrate",rgyrate) > > Hope it helps, > > Tsjerk  Thomas Holder MPI for Developmental Biology Spemannstr. 35 D72076 Tübingen 