Hi Andrew, thank you for your answer: now I have a clue! I knew that the structure is a NMR model, but what I didn't understand was that some atoms were repeated (with different coordinates). Now I have pruned my structure file and I can see a much more acceptable structure.
Thank you very much, Annalisa 2008/12/19 Andrew Purkiss-Trew <[email protected]> > Hi Annalisa, > > Is the original coordinate file an NMR structure? It looks to me like > there are several copies of each atom, which is consistent with the pdb > file resulting from an NMR refinement. These will usually have several > different models of the peptide, all consistent with the NMR data. > > You will need to extract just one set of coordinates and look at those. > Which set of coordinates to use depends on the software used to generate > the pdb, but look for the first or the 'best' model, the pdb header > should tell you which is best. > > Hope this helps at bit > > Andrew Purkiss-Trew > > On Thu, 2008-12-18 at 15:40 +0100, annalisa bordogna wrote: > > Hi all, > > I have a little problem with the visualization of a peptide > > conformation: as you can see from the picture I enclose, the structure > > appears as if every atom is bound to every neighbour atom. What (and > > how) can I set in PyMOL, to visualize a correct structure? > > > > Thank you very much for your help. > > Best regards, > > Annalisa > > > > ------------------------------------------------------- > > Annalisa Bordogna > > Ph.D. Student > > Università degli Studi di Milano - Bicocca > > Milano, IT > > > ------------------------------------------------------------------------------ > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, > Nevada. > > The future of the web can't happen without you. Join us at MIX09 to help > > pave the way to the Next Web now. Learn more and register at > > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > > _______________________________________________ PyMOL-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/pymol-users > >
