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 Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 12 Nov 2012, at 11:01, vellieux wrote: > Hello, > > 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. > > HTH, > > Fred. > > 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. >> >> Regards, >> KS > > > -- > Fred. Vellieux (B.Sc., Ph.D., hdr) > IBS / ELMA > 41 rue Jules Horowitz > F-38027 Grenoble Cedex 01 > Tel: +33 438789605 > Fax: +33 438785494 >
