[phenixbb] histidine flip in refinement

Pavel Afonine pafonine at lbl.gov
Tue Jul 21 19:04:39 PDT 2015

Hi Joel,

as was suggested main.nqh_flips=False should disable this.

However I'm puzzled about this. NQH flips functionality is designed to 
flip these residues such that the clashes are minimized and plausible 
H-bonding is achieved. So I wonder why it is not working in your case?

Would it be possible to send me input files (off list) so that I can 
reproduce this and investigate. Also please indicate HIS in question.


On 7/21/15 02:07, Joel Tyndall wrote:
> Hi all,
> We are trying to optimise a histidine interaction where NE2 would 
> ideally make a hydrogen bond with an adjacent tyrosine hydroxyl. The 
> starting point contains the hydrogen bond. However upon refinement the 
> ring flips (chi2 x 180 degrees) to place the CE1 adjacent to the 
> tyrosine hydroxyl.
> Is it possible to stop this as I see no reason why phenix.refine would 
> want to do this
> Regards
> Joel

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