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 <a.purkiss@mail.cryst.bbk.ac.uk>
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
> UniversitÓ degli Studi di Milano - Bicocca
> Milano, IT
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