[phenixbb] Something that came up on the CCP4 list...
s.kolstoe at UCL.AC.UK
Thu Sep 16 13:41:29 PDT 2010
Just for the record I've had it make a big difference a number of
times as well with both refmac & shelx. I was under the impression
that phenix.refine was "cleverly" allowing me to use that trick by
just starring the add riding hydrogens in the def file however it
seems not - something worth knowing!
On 16 Sep 2010, at 20:01, Phil Jeffrey wrote:
> I've had it make a big difference in certain circumstances. And in
> other circumstances not so much. Definitely worth a try. I do not
> use the technique routinely.
> Phil Jeffrey
> On 9/16/10 11:49 AM, Simon Kolstoe wrote:
>> So just to clarify further - if i am having problems with the final
>> geometry of a model (eg clashscore as reported by molprobity), is
>> it an
>> appropriate trick to add hydrogens and then refine in phenix.refine
>> using the riding hydrogens option, or does this not really change
>> On 16 Sep 2010, at 14:26, Pavel Afonine wrote:
>>> Hi Simon,
>>>> Could I just seek some clarification? I was under the impression
>>>> phenix.refine calculated riding hydrogens by default and took these
>>>> into account as a restraint on the geometry?
>>> if you want hydrogen atoms to be used in refinement (as "riding
>>> or explicit) your need to make sure the PDB file that you give to
>>> phenix.refine contains H atoms. That is you need to add them using
>>> programs like phenix.reduce or phenix.ready_set or using
>>> functionality in the GUI.
>>> phenix.refine will not add them internally as part of refinement IF
>>> hydrogen atoms are NOT present in input PDB file.
>>> Adding hydrogen atoms as 'riding model' does not add any refinable
>>> parameters, but the scattering contribution from them is included
>>> of the time. This is why we do not use H atoms silently but require
>>> them to be in input PDB file - simply to make sure the reported
>>> statistics (such as R-factors) is easily reproducible.
>>> All the best!
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
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