Dear All, Suppose my protein has 4 same subunits (not exactly 4 subunits, in order to explain things clear, it contains not less than 2 identical subunitss), each subunit has the potential H-bond involving N of HIS. I have run the optimization by both PDB_REDO and the Phenix refine with the phenix flips checked. I have checkecd the PDB_REDO refine results and the Phenix refine results, the answer is, suppose in PDB_REDO it tells us subunit A has that specific H-bond formed, Phenix refine rells us that subunit B has that specific H-bond formed. In fact, supposing it has 4 subunits, the symmetry determines that the 4 subunits should be identical, and they should all contains the specific H-bonds, or all do not contains the specific H-bonds. Any more suggestions welcome. Smith
At 2015-05-20 22:55:13, "Robbie Joosten" <[email protected]> wrote: Hi Smith, Just to contrast Pavel's phenix plug. PDB_REDO does HQN-flips automatically based on WHAT _CHECK results and refines your model in Refmac. Cheers, Robbie Sent with my Windows Phone Van: Robbie Joosten Verzonden: 20-5-2015 14:30 Aan: Smith Liu; [email protected] Onderwerp: RE: [ccp4bb] HIS related crystallography issue You can typically assign the histidine orientation based on analysis of the hydrogen bond network. In ambiguous cases you might have to look a few residues deep. WHAT_CHECK does this for you by a global optimization of the hydrogen bond network. Cheers, Robbie Sent with my Windows Phone Van: Smith Liu Verzonden: 20-5-2015 14:12 Aan: [email protected] Onderwerp: [ccp4bb] HIS related crystallography issue Dear All, Suppose the protein crystal resolution is about 2-3A, then in the map it should be rather difficult to distinguish the C and N in the sidechain of HIS. In this way we may regard the sidechain of HIS is flippable. But suppose in one flipped conformation of the HIS, the free N in the sidechain of HIS can form H-bond with the neighbour H of the OH of the Thr, in the other flipped conformation of the HIS, the free N in the sidechain of HIS cannot form H-bond with the neighbour H of the OH of the Thr (caused by distance issue). Suppose whether the H-bond forms between the free N in the sidechain of HIS and the neighbour H of the OH of the Thr was very important biologically, in this situation how can we distinguish whether the H-bond forms? Smith
