[phenixbb] histidine flip in refinement

Jrh jrhelliwell at gmail.com
Wed Jul 22 03:24:08 PDT 2015


Dear Smith,
These two articles will offer you the possibility to do what you wish for non-covalent atom pairs:-
http://dx.doi.org/10.1107/S1600576715006287
http://dx.doi.org/10.1107/S2052252513031485 
Best wishes,
John 

Emeritus Prof John R Helliwell DSc_Physics 
FInstP FRSC FSocBiol Fellow of the ACA
Emeritus Member of the British Biochemical Society
School of Chemistry, University of Manchester, M13 9PL, UK.


On 22 Jul 2015, at 10:36, "Smith Liu" <smith_liu123 at 163.com> 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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