Anna, 
If possible try a different, perhaps more modern structure than 5PTI.
Leif

On Fri, Jan 16, 2015 at 12:33 PM, Tim Gruene <tg@shelx.uni-ac.gwdg.de> wrote:
Hi Anna,

which version of Phenix are you using? If it is from before 2012'ish,
you may fix this by updating Phenix.

Cheers,
Tim

On 01/16/2015 05:32 PM, Anna Makal wrote:
> Hi,
>
> I have just done a joint x-ray / neutron refinement in Phenix using 5PTI
> structure and data from PDB.
> The input contains H atoms, with positions as refined against neutron
> dataset.
>
> In the resulting model, all H atoms ended up in 'idealized X-ray'
> positions (C-H distance of 0.96A), just as they would if I performed
> refinement against xray data only with riding model for H hydrogen atoms.
>
> Is it possible to run joint X-ray neutron refinement in such a manner
> that final H atoms positions are based on neutron data?
>
> Regards,
>
> Anna Makal
>
>
>
>
>
>
>
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--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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