[phenixbb] histidine flip in refinement

Pavel Afonine pafonine at lbl.gov
Tue Jul 21 21:26:09 PDT 2015


Hi Smith,

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 
interpret).

Pavel

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.
>
> Smith
>
>
>
>
>
> 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
>     question.
>
>     Thanks,
>     Pavel
>
>     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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