Also, a very small fraction of amino acids have torsion angles that are really outside normal ranges, as demonstrated by high resolution structures.
If the density is convincing, leave them as they are.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
On 12 Nov 2012, at 11:01, vellieux wrote:
> There are examples of regions (such as loops) where the electron density is rather "poor" and does not allow to build a proper model of the polypeptide chain (the refinement program cannot fit a satisfactory model in that area). Hence you just know that the chain "goes through there" and you cannot "fix it". Usually there are relatively high temperature factors associated with such regions. This could be what you have in your structure. In this case I would deposit and add a remark in the header region of the PDB file to explain. If this has been observed in other structures then what you observe is consistent with the previous observations.
> On 12/11/12 10:54, Krithika Sundaram wrote:
>> Hi all,
>> I am currently validating my protein and experiencing a few issues. I am unable to fix the torsion angles for eight residues no matter what I try. There are 3 models deposited on the PDB website belonging to the same protein. Five of the residues’ torsion angles (of the eight) are consistently reported as being problematic by PDB validation server for all three models.
>> I have tried deleting these residues and adding them again after refinement, but the problem doesn't disappear. I have spent a few weeks looking at this and trying every possible solution to this problem.
>> Just wondering what else I can try to fix the issues reported!
>> Thanks in advance.
> Fred. Vellieux (B.Sc., Ph.D., hdr)
> IBS / ELMA
> 41 rue Jules Horowitz
> F-38027 Grenoble Cedex 01
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