Dear Mahesh,
Are all the structures at similar resolution? Definition of secondary structure is, and can be, affected by the level of geometric restraints/constraints used in the refinement process.
Tony.
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Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ
email: [log in to unmask]
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512
On Oct 21, 2013, at 11:55 AM, Mahesh Lingaraju wrote:
> Hello experts
>
> Thanks for your insights.
> For one of the structures, it turned out to be a rendering issue by pymol like matt pointed out. For the other, the residues are clearly in a less than ideal position. Even if I see deviation from the RMSD plots, i cannot be sure that the structure were refined ideally at those positions ( those are not my structures, i just have the pdb files from my collaborator).
>
> Thanks again,
>
> Mahesh
>
> P.S from what all of you are saying it sounds like those changes are not real, if I find that they could be Ill let everyone know.
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