You can also check if there is connecting electron density, see for example the electron density server at http://eds.bmc.uu.se/eds/ . This of course only works if the authors have deposited the experimental data.
I hope this helps. Best regards, Anne -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Tsjerk Wassenaar Sent: 24. august 2006 13:36 To: mahesh kulharia Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Problem Hi Mahesh, There is no way to see whether two atoms are connected. Pymol guesses the connectivity based on the distances between the particles. But to be certain whether atoms are bonded, you have to look in the PDB file, which should mention covalent attachment of a ligand. At the end of the pdb file there will also often be CONECT statements, indicating which bonds to create explicitly. Pymol also reads those records. Alternatively, you can look up the original paper regarding the pdb structure, in which you should be able to find out more about the nature of the system. Hope it helps, Tsjerk On 8/24/06, mahesh kulharia <kulha...@googlemail.com> wrote: > Hi > I need help. Can some one tell me a way to find out whether 2 molecules are > connected by covalent linkage or not. Say for example in pdb files we have > ligand and protein molecules and I wish to know a way to find out if the > ligand is connected to the protein via a covalent bond or not, The problem > is I cannot use covalent radius values for specific bonds as the resolution > is not good in pdb. > I wonder how does the program in pymol does that. I would be very grateful > if someone could tell me a way out. Please help. > need_help > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
