-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear KS,
in addition to what Mark said, you might think about why the torsion angles are this way, i.e. there might be interactions which twist your protein into that conformation. Only because something is reported as off-standard does not mean it is wrong! Regards, Tim On 11/12/2012 12:02 PM, Mark J van Raaij wrote: > 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 >> > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQoOLdUxlJ7aRr7hoRAs6jAJ0Whkkp3sVxJM+5zPgIhB4zdwMSKwCfV1Vp cbUAmMXW3A1dlo71ro9b5eA= =NHjy -----END PGP SIGNATURE-----
