[phenixbb] histidine flip in refinement

Smith Liu smith_liu123 at 163.com
Wed Jul 22 02:36:55 PDT 2015

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.


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).


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.


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.


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





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