IL.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 ridin
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
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 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 electro
'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
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
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.
Che
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 a
