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. --- 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: antony.oli...@sussex.ac.uk 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. > > > > >
