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 Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: [email protected] tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On 1/12/12 11:14 PM, "Tim Fenn" <[email protected]> wrote: >On Thu, Jan 12, 2012 at 8:11 AM, Pavel Afonine <[email protected]> wrote: >> >>> Who needs hydrogens? >> >> >> may be you need to read this (for example): >> >> http://www.phenix-online.org/papers/dz5209_reprint.pdf >> > >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
