[phenixbb] Real Space R value

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Sep 3 07:03:47 PDT 2008

Hi Matthew,

You can also use phenix.get_cc_mtz_pdb with a ligand...it should treat the
ligand as a single residue.

Mark also asked offline about alternate conformations...here is my answer
to that:

If there is only on N for each residue, it will average over all atoms in
all conformations. If there are multiple N atoms, and all atoms for each
conformer are grouped, it will write out the residue twice. If there  are
multiple N atoms and they are interspersed, it will give an incorrect
answer (it will write out the residue twice but the cc values will not be
for the two conformers).

All the best,
Tom T

> Hi,
> Yes, you can use phenix.get_cc_mtz_pdb (see phenix.doc)
> But I wonder if there is a way to get CC value for a ligand or a metal
> ion too ??
> Nigel ???
>> Date: Tue, 2 Sep 2008 13:18:59 -0400
>> From: "nih\mayerm" <mayerm at mail.nih.gov>
>> Subject: [phenixbb] Real Space R value
>> To: phenixbb at phenix-online.org
>> Message-ID: <FEAAD2DC-1906-4194-881B-CA83B48E8043 at mail.nih.gov>
>> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>> Is it possible to calculate a list of Real Space R values for
>> structures refined with phenix.refine ?
>> If so advice on how to do this would be greatly appreciated.
>> Thanks - Mark Mayer
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