From: Antony Oliver
Date: 12 January 2012 11:52
----------
From: Pavel Afonine
Tony,
----------
From: Antony Oliver
----------
From: Tim Fenn
While this reference is useful, it neglects the role of prior chemical
forces (vdW and electrostatics, for example) in positioning hydrogen
atoms. The X-ray/neutron data is often not sufficient to uniquely
define an atomic position (hydrogen or otherwise), which can be
especially problematic for atoms with several degrees of freedom, like
water or a hydroxyl hydrogen. Force fields have come a long way in
defining these forces with reasonable chemical accuracy in the past 10
years, and there is work to show this does benefit X-ray/neutron
refinement (e.g. http://dx.doi.org/10.1016/j.str.2011.01.015) -
suggesting its worthwhile to include this information in X-ray target
functions. At the very least, it should not be left out of the
discussion, especially when hydrogen atoms are concerned!!!
Regards,
Tim
----------
From: Antony Oliver
Ok, I'm completed baffled... and have obviously started something
unintentionally...
NB: it was a joke!
I was amused that Molprobity, after 'adding' hydrogens to my model, had
'improved' the clashscore of my model by an obviously unnecessary number
of decimal places...!
[0.0099999999999998 point apparently].
Just me apparently.
Off to put my head in a cardboard box.
T.
---
Dr Antony W Oliver
Date: 12 January 2012 11:52
Dear fellow Xtallographers.
I love Molprobity, but I have to say this did make me chuckle (see attached jpeg file). Who needs hydrogens?
Tony.
---
Dr Antony W Oliver
----------
From: Pavel Afonine
Tony,
Who needs hydrogens?
may be you need to read this (for example):
?
Pavel
----------
From: Antony Oliver
Pavel and CCP4ers.
I did have my tongue firmly in my cheek when mentioning the hydrogens…
I am well aware of their importance [winking smiley]
----------
From: Tim Fenn
While this reference is useful, it neglects the role of prior chemical
forces (vdW and electrostatics, for example) in positioning hydrogen
atoms. The X-ray/neutron data is often not sufficient to uniquely
define an atomic position (hydrogen or otherwise), which can be
especially problematic for atoms with several degrees of freedom, like
water or a hydroxyl hydrogen. Force fields have come a long way in
defining these forces with reasonable chemical accuracy in the past 10
years, and there is work to show this does benefit X-ray/neutron
refinement (e.g. http://dx.doi.org/10.1016/j.str.2011.01.015) -
suggesting its worthwhile to include this information in X-ray target
functions. At the very least, it should not be left out of the
discussion, especially when hydrogen atoms are concerned!!!
Regards,
Tim
----------
From: Antony Oliver
Ok, I'm completed baffled... and have obviously started something
unintentionally...
NB: it was a joke!
I was amused that Molprobity, after 'adding' hydrogens to my model, had
'improved' the clashscore of my model by an obviously unnecessary number
of decimal places...!
[0.0099999999999998 point apparently].
Just me apparently.
Off to put my head in a cardboard box.
T.
---
Dr Antony W Oliver
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