Hi Young-Jin, why don't you try two refinement runs using two different CIF files for ATP where different P-O bond lengths are defined (just edit CIF files manually): phenix.refine model.pdb data.mtz atp_1.cif output.prefix=atp_1 phenix.refine model.pdb data.mtz atp_2.cif output.prefix=atp_2 ? Then see which one produces a better result locally (R-factors will not show this). If you don't see any difference than the resolution or/and data quality do not allow distinguishing this level of detail. Pavel. On 5/19/09 8:42 AM, Young-Jin Cho wrote:
Hello phenix users,
I am wondering if phenix.elbow can attach H onto phosphate group for refinement. The reason for that, based on different pH environment, phosphate group should have different charges with respect to how many protons attached.
In addition, how can I know normal distance restraints such as ATP? What I only know from the coot is that it shows P-O bond length is 1.61A and P-O bond (delocalized double bond) is 1.5A. The reason for this is, I heard about phosphate ion, if it is protonated, then the bond length of HO-P is longer than that of non-protonated O-P. I want to try if is true for ATP as well. Is there anyone who knows practically testing this fact by using phenix?
Thanks in advance,
YoungJin
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