[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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