Being of an untrusting disposition, I would ask your collaborator for the reflection data as well as the PDBs - it is always a good idea to look at the maps when there is some unexpected structural feature! - The DB provides an electron density server, if the structures have been deposited, otherwise it is straightforward to generate a map yourself and look at it in coot. Eleanor Dodson
On 21 October 2013 13:53, Antony Oliver <antony.oli...@sussex.ac.uk> wrote: > 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. >> >> >> >> >>
