[phenixbb] histidine flip in refinement

Pavel Afonine pafonine at lbl.gov
Wed Jul 22 10:56:08 PDT 2015


Hi Smith,

this may be helpful:

https://www.phenix-online.org/papers/wd5073_reprint.pdf

Pavel

On 7/22/15 02:36, Smith Liu wrote:
> Dear Pavel,
>
> Thanks for your interpretation. But for most of the crystal structure, 
> they were got from 2-4 A crystal rather than from around 1 A 
> crystal. Then how can we analyse the non-covalent bonds based on the 
> 3-D crystal structure? As I know, there were crystal papers which 
> analyse non-covalent bonds or protein-protein interaction based on the 
> 3-D crystal structure.
>
> Best regards.
>
> Smith
>
>
>
>
>
>
> At 2015-07-22 12:26:09, "Pavel Afonine" <pafonine at lbl.gov> wrote:
>
>     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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