Re: [ccp4bb] CH-bond length discrepancies

[Robbie Joosten]

Hi Bernhard,

You touch a valid point. You get different clash scores in MP depending on how 
you add hydrogens when you run it (unless this was solved recently). So you can 
essentially cheat the program by choosing a different H addition function. I 
don't get why this option exists at all. If you add hydrogens to your model you 
should do it in such a way that your validation algorithm gives a reliable 
answer.

For what it is worth, I think hydrogens should be modelled where they are, not 
where we observe them. That means for X-ray we need a correction along the the 
bond, for neutron diffraction we don't, and for electron diffraction, well that 
gets a bit more complicated.

Cheers,
Robbie


Sent from my Windows 10 phone

Van: Bernhard Rupp<mailto:hofkristall...@gmail.com>
Verzonden: zaterdag 29 april 2017 21:18
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: Re: [ccp4bb] CH-bond length discrepancies

Thanks to all respondents.

It seems the source of the discrepancy is that some programs use nuclear 
distances and some use electron density peak distances.

Now, does it matter, for example, using  nuclear distances for placing riding 
Hs in the VdW terms,
(i.e., a model for dipole interactions which are largely electronically 
dominated) and then validate
against X-ray (i.e. electronic) distances? If this use of different distance 
sets were consistent (I am not even sure of that),
then we would probably introduce systematic bias.

The point is probably academic in practical terms but somehow it would be 
interesting
to understand how using which distances when is justified…

Best, BR

From: Zhijie Li [mailto:zhijie...@utoronto.ca]
Sent: Friday, April 28, 2017 3:42 PM
To: b...@hofkristallamt.org
Subject: Re: [ccp4bb] CH-bond length discrepancies


Hi Bernhard,

I believe this is the data you are interested:

http://journals.iucr.org/b/issues/2010/03/00/so5037/so5037.pdf

Zhijie

On 28/04/2017 1:33 PM, Bernhard Rupp wrote:
Dear Fellows of the Bond,

when validating a QM refined homology model with Molprobity, I noticed various 
8 sigma deviations in the carbon-hydrogen bond distances.
Out of curiosity, I then used refmac to calculate riding Hs for the same model, 
and at least in one instance (N-H backbone) there are
significant differences between Molprobity and Refmac H bond distances 
(differences to the QM distances in other
instances I find interesting, but less relevant for us).

The riding H vs Molprobity presumably should be consistent, because if we use 
them in VDW restraints but
they differ from the validation target, systematic bias will occur. I have no 
feel how significant that effect
might be – maybe someone more erudite can comment.

Examples

distance  MP   REF QM
backbone N-H   0.861.011.00
phenyl C-H 0.930.931.09

Best, BR

PS: If someone has accurate experimental values for CH distances I’d appreciate 
a link.
No access to CSD.

--
Bernhard Rupp
Crystallographiae Vindicis Militum Ordo
http://www.hofkristallamt.org/
b...@hofkristallamt.org<mailto:b...@hofkristallamt.org>
+1 925 209 7429
+43 767 571 0536
--
Many plausible ideas vanish
at the presence of thought
--

Re: [ccp4bb] CH-bond length discrepancies

[Bernhard Rupp]

Thanks to all respondents.

 

It seems the source of the discrepancy is that some programs use nuclear
distances and some use electron density peak distances.

 

Now, does it matter, for example, using  nuclear distances for placing
riding Hs in the VdW terms,

(i.e., a model for dipole interactions which are largely electronically
dominated) and then validate

against X-ray (i.e. electronic) distances? If this use of different distance
sets were consistent (I am not even sure of that), 

then we would probably introduce systematic bias.

 

The point is probably academic in practical terms but somehow it would be
interesting

to understand how using which distances when is justified.

 

Best, BR

 

From: Zhijie Li [mailto:zhijie...@utoronto.ca] 
Sent: Friday, April 28, 2017 3:42 PM
To: b...@hofkristallamt.org
Subject: Re: [ccp4bb] CH-bond length discrepancies

 

Hi Bernhard,

I believe this is the data you are interested:

http://journals.iucr.org/b/issues/2010/03/00/so5037/so5037.pdf

Zhijie

 

On 28/04/2017 1:33 PM, Bernhard Rupp wrote:

Dear Fellows of the Bond,

 

when validating a QM refined homology model with Molprobity, I noticed
various 8 sigma deviations in the carbon-hydrogen bond distances.

Out of curiosity, I then used refmac to calculate riding Hs for the same
model, and at least in one instance (N-H backbone) there are 

significant differences between Molprobity and Refmac H bond distances
(differences to the QM distances in other 

instances I find interesting, but less relevant for us).

 

The riding H vs Molprobity presumably should be consistent, because if we
use them in VDW restraints but

they differ from the validation target, systematic bias will occur. I have
no feel how significant that effect

might be - maybe someone more erudite can comment.

 

Examples

 

distance  MP   REF QM

backbone N-H   0.861.011.00   

phenyl C-H 0.930.931.09

 

Best, BR

 

PS: If someone has accurate experimental values for CH distances I'd
appreciate a link.

No access to CSD.

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 767 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

Re: [ccp4bb] CH-bond length discrepancies

[Pavel Afonine]

Also, see figure 4 here:
http://phenix-online.org/papers/dz5209_reprint.pdf
that illustrates the difference.
Pavel

On Fri, Apr 28, 2017 at 10:33 AM, Bernhard Rupp 
wrote:

> Dear Fellows of the Bond,
>
>
>
> when validating a QM refined homology model with Molprobity, I noticed
> various 8 sigma deviations in the carbon-hydrogen bond distances.
>
> Out of curiosity, I then used refmac to calculate riding Hs for the same
> model, and at least in one instance (N-H backbone) there are
>
> significant differences between Molprobity and Refmac H bond distances
> (differences to the QM distances in other
>
> instances I find interesting, but less relevant for us).
>
>
>
> The riding H vs Molprobity presumably should be consistent, because if we
> use them in VDW restraints but
>
> they differ from the validation target, systematic bias will occur. I have
> no feel how significant that effect
>
> might be – maybe someone more erudite can comment.
>
>
>
> Examples
>
>
>
> distance  MP   REF QM
>
> backbone N-H   0.861.011.00
>
> phenyl C-H 0.930.931.09
>
>
>
> Best, BR
>
>
>
> PS: If someone has accurate experimental values for CH distances I’d
> appreciate a link.
>
> No access to CSD.
>
>
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429 <(925)%20209-7429>
>
> +43 767 571 0536 <+43%207675%20710536>
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>

Re: [ccp4bb] CH-bond length discrepancies

[Santarsiero, Bernard D.]

It totally depends on what you define as your C-H bond length.

For XRD work, the C-H is the distance between the electron
center-of-masses. For  neutron or high-resolution XRD work, you can
determine the distance between the nuclear center-of-masses.  They are
different by about 0.1A.  The electron COM for hydrogen is substantially
shifted along the bond towards the carbon atom.

I did a very precise determination of 1,1-dicyclobutanedicarboxylic acid
at 20K, and the C-H bond lengths averaged to 0.991A, and far shorter than
the 1.096A you'd expect from a neutron diffraction study.

The VDW distances shouldn't be that important since the potential isn't
that sensitive with a difference of 0.1A.  If you have to restrain C-H
distances for XRD refinement, then they should be shortened.

BDS



On Sat, April 29, 2017 8:22 am, benjamin bax wrote:
>
>
>
> 'Most distances   between bonded  atoms   weresettled longago 
> to  highaccuracy,   but,in  the caseof  
> hydrogens,  the values  in  common  use often   differ  by
>   as  muchas  20%.'
>
> Phenix/   MolProbity  HydrogenParameter   Update
>
> Deis, L. N., Verma, V., Videau, L. L., Prisant, M. G., Moriarty, N. W.,
>
> Headd, J. J., Chen, V. B., Adams, P. D., Snoeyink, J., Richardson, J. S. &
> Richardson, D. C. (2013). Comput. Crystallogr. Newsl. 4, 9–10.
>
>
>
> On 28 Apr 2017, at 18:33, Bernhard Rupp  wrote:
>
> Dear Fellows of the Bond,
>
> when validating a QM refined homology model with Molprobity, I noticed
> various 8 sigma deviations in the carbon-hydrogen bond distances.
> Out of curiosity, I then used refmac to calculate riding Hs for the same
> model, and at least in one instance (N-H backbone) there are
> significant differences between Molprobity and Refmac H bond distances
> (differences to the QM distances in other
> instances I find interesting, but less relevant for us).
>
> The riding H vs Molprobity presumably should be consistent, because if we
> use them in VDW restraints but
> they differ from the validation target, systematic bias will occur. I have
> no feel how significant that effect
> might be – maybe someone more erudite can comment.
>
> Examples
>
> distance  MP   REF QM
> backbone N-H   0.861.011.00
> phenyl C-H 0.930.931.09
>
> Best, BR
>
> PS: If someone has accurate experimental values for CH distances I’d
> appreciate a link.
> No access to CSD.
>
> --
> Bernhard Rupp
> Crystallographiae Vindicis Militum Ordo
> http://www.hofkristallamt.org/ 
> b...@hofkristallamt.org 
> +1 925 209 7429
> +43 767 571 0536
> --
> Many plausible ideas vanish
> at the presence of thought
> --
>
>
> Dr Ben Bax
>
> York Structural Biology Laboratory,
> Department of Chemistry,
> University of York,
> York YO10 5DD
>
> ben.d.v@gmail.com
>
>
>
>
>
>


-- 
Bernard D. Santarsiero
Associate Director, UI Health Systems Biorepository
Research Professor
Center for Biomolecular Sciences and the
  Department of Medicinal Chemistry and Pharmacognosy
Center for Structural Biology
Center for Clinical and Translational Science
University of Illinois at Chicago
MC870  3070MBRB  900 South Ashland Avenue
Chicago, IL 60607-7173  USA
(312) 413-0339 (office)
(312) 413-9303 (FAX)
http://www.uic.edu/labs/bds
http://scholar.google.com/citations?user=fGauLBMJ

Re: [ccp4bb] CH-bond length discrepancies

[benjamin bax]

'Most   distances   between bonded  atoms   weresettled longago 
to  highaccuracy,   but,in  the caseof  
hydrogens,  the values  in  common  use often   differ  by  
as  muchas  20%.'

Phenix  /   MolProbity  HydrogenParameter   Update

Deis, L. N., Verma, V., Videau, L. L., Prisant, M. G., Moriarty, N. W.,

Headd, J. J., Chen, V. B., Adams, P. D., Snoeyink, J., Richardson, J. S. & 
Richardson, D. C. (2013). Comput. Crystallogr. Newsl. 4, 9–10. 



On 28 Apr 2017, at 18:33, Bernhard Rupp  wrote:

Dear Fellows of the Bond,
 
when validating a QM refined homology model with Molprobity, I noticed various 
8 sigma deviations in the carbon-hydrogen bond distances.
Out of curiosity, I then used refmac to calculate riding Hs for the same model, 
and at least in one instance (N-H backbone) there are 
significant differences between Molprobity and Refmac H bond distances 
(differences to the QM distances in other 
instances I find interesting, but less relevant for us).
 
The riding H vs Molprobity presumably should be consistent, because if we use 
them in VDW restraints but
they differ from the validation target, systematic bias will occur. I have no 
feel how significant that effect
might be – maybe someone more erudite can comment.
 
Examples
 
distance  MP   REF QM
backbone N-H   0.861.011.00   
phenyl C-H 0.930.931.09
 
Best, BR
 
PS: If someone has accurate experimental values for CH distances I’d appreciate 
a link.
No access to CSD.
 
--
Bernhard Rupp
Crystallographiae Vindicis Militum Ordo
http://www.hofkristallamt.org/ 
b...@hofkristallamt.org 
+1 925 209 7429
+43 767 571 0536
--
Many plausible ideas vanish 
at the presence of thought
--


Dr Ben Bax

York Structural Biology Laboratory, 
Department of Chemistry, 
University of York,
York YO10 5DD

ben.d.v@gmail.com

 

 

Re: [ccp4bb] CH-bond length discrepancies

[Pavel Afonine]

Note, Molprobity has an option to use longer (neutron) X-H distances.
Pavel

On Fri, Apr 28, 2017 at 11:46 AM, Tristan Croll  wrote:

> I believe the reason for the discrepancy here is that MolProbity by
> default places the hydrogens according to the centroid of the electron
> cloud (most relevant to x-ray crystallographic data) rather than the
> nuclear position. In a polar bond like N-H the difference can be quite
> substantial.
>
> Cheers,
>
> Tristan
>
>
>
> Tristan Croll
> Research Fellow
> Cambridge Institute for Medical Research
> University of Cambridge CB2 0XY
>
>
>
>
> On 28 Apr 2017, at 18:33, Bernhard Rupp  wrote:
>
> Dear Fellows of the Bond,
>
>
>
> when validating a QM refined homology model with Molprobity, I noticed
> various 8 sigma deviations in the carbon-hydrogen bond distances.
>
> Out of curiosity, I then used refmac to calculate riding Hs for the same
> model, and at least in one instance (N-H backbone) there are
>
> significant differences between Molprobity and Refmac H bond distances
> (differences to the QM distances in other
>
> instances I find interesting, but less relevant for us).
>
>
>
> The riding H vs Molprobity presumably should be consistent, because if we
> use them in VDW restraints but
>
> they differ from the validation target, systematic bias will occur. I have
> no feel how significant that effect
>
> might be – maybe someone more erudite can comment.
>
>
>
> Examples
>
>
>
> distance  MP   REF QM
>
> backbone N-H   0.861.011.00
>
> phenyl C-H 0.930.931.09
>
>
>
> Best, BR
>
>
>
> PS: If someone has accurate experimental values for CH distances I’d
> appreciate a link.
>
> No access to CSD.
>
>
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429 <(925)%20209-7429>
>
> +43 767 571 0536 <+43%207675%20710536>
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
>

Re: [ccp4bb] CH-bond length discrepancies

[Tristan Croll]

I believe the reason for the discrepancy here is that MolProbity by default 
places the hydrogens according to the centroid of the electron cloud (most 
relevant to x-ray crystallographic data) rather than the nuclear position. In a 
polar bond like N-H the difference can be quite substantial.

Cheers,

Tristan

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 28 Apr 2017, at 18:33, Bernhard Rupp  wrote:
> 
> Dear Fellows of the Bond,
>  
> when validating a QM refined homology model with Molprobity, I noticed 
> various 8 sigma deviations in the carbon-hydrogen bond distances.
> Out of curiosity, I then used refmac to calculate riding Hs for the same 
> model, and at least in one instance (N-H backbone) there are
> significant differences between Molprobity and Refmac H bond distances 
> (differences to the QM distances in other
> instances I find interesting, but less relevant for us).
>  
> The riding H vs Molprobity presumably should be consistent, because if we use 
> them in VDW restraints but
> they differ from the validation target, systematic bias will occur. I have no 
> feel how significant that effect
> might be – maybe someone more erudite can comment.
>  
> Examples
>  
> distance  MP   REF QM
> backbone N-H   0.861.011.00  
> phenyl C-H 0.930.931.09
>  
> Best, BR
>  
> PS: If someone has accurate experimental values for CH distances I’d 
> appreciate a link.
> No access to CSD.
>  
> --
> Bernhard Rupp
> Crystallographiae Vindicis Militum Ordo
> http://www.hofkristallamt.org/
> b...@hofkristallamt.org
> +1 925 209 7429
> +43 767 571 0536
> --
> Many plausible ideas vanish
> at the presence of thought
> --
>  

[ccp4bb] CH-bond length discrepancies

[Bernhard Rupp]

Dear Fellows of the Bond,

 

when validating a QM refined homology model with Molprobity, I noticed
various 8 sigma deviations in the carbon-hydrogen bond distances.

Out of curiosity, I then used refmac to calculate riding Hs for the same
model, and at least in one instance (N-H backbone) there are 

significant differences between Molprobity and Refmac H bond distances
(differences to the QM distances in other 

instances I find interesting, but less relevant for us).

 

The riding H vs Molprobity presumably should be consistent, because if we
use them in VDW restraints but

they differ from the validation target, systematic bias will occur. I have
no feel how significant that effect

might be - maybe someone more erudite can comment.

 

Examples

 

distance  MP   REF QM

backbone N-H   0.861.011.00   

phenyl C-H 0.930.931.09

 

Best, BR

 

PS: If someone has accurate experimental values for CH distances I'd
appreciate a link.

No access to CSD.

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 767 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--