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
