Re: [phenixbb] histidine flip in refinement

22 Jul 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"  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"  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