[phenixbb] histidine flip in refinement
pafonine at lbl.gov
Tue Jul 21 21:26:09 PDT 2015
2-3 A is not atomic resolution, so you cannot meaningfully measure
distances between individual atoms in your model at this resolution, I
think (I guess it is safer to say that you can measure these distances,
technically, but their meaning is not going to be straightforward to
On 7/21/15 20:10, Smith Liu wrote:
> Dear Pavel,
> Related to Joel's question, suppose the resolution is about 2-3 A, and
> I have added H (should be modelled "H"）for the refinement. If I want
> to measure the H-bond length between the NE2 and H of OH of Tyr, I
> need to measure the distance between NE2 and the "modelled H" of OH of
> Tyr. Is this "modelled H" position reliable for the length measurement
> of the H-bond?
> Best regards.
> At 2015-07-22 10:04:39, "Pavel Afonine" <pafonine at lbl.gov> wrote:
> 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
> 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
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