[phenixbb] Something that came up on the CCP4 list...

Simon Kolstoe s.kolstoe at ucl.ac.uk
Thu Sep 16 01:42:00 PDT 2010

In the fascinating current discussion on the ccp4 list Pavel said:

 >Dear Ed,
 >no, if you start with model that has no hydrogens, they will not be  
generated internally.
On 9/15/10 2:58 PM, Ed Pozharski wrote:
> Sure.  But if I start with model that has no hydrogens, they will be
> generated but not passed to the output, right.  just like refmac.
> On Wed, 2010-09-15 at 14:52 -0700, Pavel Afonine wrote:
>> Dear Ed,
>> On 9/15/10 2:47 PM, Ed Pozharski wrote:
>>> On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote:
>>>> So the riding hydrogen model is imperfect.  At least with
>>>> phenix.refine
>>>> you can measure it, unlike the default behavior of REFMAC.  (But  
>>>> you
>>>> can
>>>> tell it to write hydrogens out, I believe).
>>> My impression is that default behavior of phenix.refine is the  
>>> same - I
>>> had to change parameters to include hydrogens in the output.
>> No, if your input file contains H atoms, the output file will contain
>> them too (in phenix.refine). You don't have to change any  
>> parameters for
>> this.
>> Pavel.

Could I just seek some clarification? I was under the impression that  
phenix.refine calculated riding hydrogens by default and took these  
into account as a restraint on the geometry?


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