[phenixbb] Attaching H onto phosphate group and ATP

Pavel Afonine PAfonine at lbl.gov
Mon May 25 16:06:23 PDT 2009

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 

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.


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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