[phenixbb] Attaching H onto phosphate group and ATP

[Ralf W. Grosse-Kunstleve]

Hi YoungJin,

The elbow author, Nigel, is out of email reach this week and next. In
the meantime I'll offer what I know...

> 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.

You can try out elbow's capabilities like this:

  phenix.elbow --key atp --opt

Note that you get a slightly different result each time you run it;
you may want to try a few runs and compare.

> In addition, how can I know normal distance restraints such as ATP?

You can find the ATP restraints definitions like this:

  phenix.where_mon_lib_list_cif
  cd <what you see minus the last two components of the path>
  cd a
  more ATP.cif

If you run phenix.refine, you can inspect the restraints used by
looking at the .geo file.

> 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.

I'm not sure if eblow handles the delocalization. You could run elbow
for your molecule to get a starting .cif file, then modify manually
following the standard ATP.cif file.

Ralf