Re: [PyMOL] Center of mass
Enter editing mode, select the 2 points, press Ctrl + t or type bond on the cli. Cheers, Marius On Thu, Mar 31, 2011 at 11:36 AM, kanika sharma ksharma...@gmail.comwrote: I have two points corresponding to center of masses of 2 proteins. I have to draw a line between both. Is there a feature that can do this? -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Center of mass
This says that bond can only be added within an object not between 2 objects. -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Center of mass
If I'm not mistaken, you can select both center of masses, since they are independent objects in the right side bar, and save them together as a single pdb. Then, when loading this single pdb, you'll be able to draw the bond. Hope that helps. This says that bond can only be added within an object not between 2 objects. -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Center of mass
Hi Kanika, You can also use pseudoatoms. If you have the positions: pseudoatom coms,pos=[x1,y1,z1] pseudoatom coms,pos=[x2,y2,z2] bond coms,coms Or, if you just have the chains: pseudoatom coms, chain a pseudoatom coms, chain b bond coms, coms Alternatively you can use CGO objects. But pseudoatoms are more versatile in this case. Hope it helps, Tsjerk On Thu, Mar 31, 2011 at 12:12 PM, Ramiro Téllez Sanz urcind...@gmail.com wrote: If I'm not mistaken, you can select both center of masses, since they are independent objects in the right side bar, and save them together as a single pdb. Then, when loading this single pdb, you'll be able to draw the bond. Hope that helps. This says that bond can only be added within an object not between 2 objects. -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] RES: radius of gyration
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:ksharma...@gmail.com] 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] RES: radius of gyration
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] # Mass-weighted 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/tmass-mm) # 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.si...@lnbio.org.br 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.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:ksharma...@gmail.com] 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Center of mass
Hi Kanika and Tsjerk, if you use the commands below: pseudoatom coms, chain a pseudoatom coms, chain b bond coms, coms you create the center of geometry rather than the center of mass. I'd like to know how to create the center of mass. Alternatively you can use the command distance to draw a line between 2 points or selections, distance name,pointA,pointB Hope it helps, Cunliang-- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] RES: radius of gyration
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] # Mass-weighted 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/tmass-mm) # 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 D-72076 Tübingen -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
