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

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" 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

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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I'm afraid I have to disagree with Pavel's statement. For a model refined to X-ray data in the 2-3 A resolution range, with stereochemical restraints, you can deduce quality information about the distances between atoms. The bond length and angle restraints do a very good job at resolving the ambiguities in fitting the blobby density. This has been routinely done for decades. A proper error analysis and estimates of the standard deviation of your measurement is a tricky proposition, I agree, but if the atoms are at full occupancy and the density is clear my "gut-level" estimate would put the sd around 0.2 to 0.3 A. If you want something more quantitative, I suggest you measure the NH--O hydrogen bond distances in some stretches of alpha-helix and compare your model's values to those of true atomic resolution models of alpha-helices. The scatter in values in your model should give a reasonable estimate of the ability of your model to "predict" other hydrogen bond distances. Dale Tronrud On 7/21/2015 9:26 PM, 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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