[phenixbb] hydrogens in riding model create steric clashes after refinement

Nathaniel Echols nechols at lbl.gov
Thu Aug 19 15:33:20 PDT 2010

On Thu, Aug 19, 2010 at 10:16 AM,  <amadrona at uci.edu> wrote:
> I know that the defualt is "riding-model" so that the hydrogen atoms are
> not refined.  However, I thought that the program would be able to avoid
> steric clashes.  Is there an aditional command I need to turn on to
> account for this?  I am currently fixing every hydrogen that clashes on an
> individual basis in coot.  There are also a handfull of hydrogens that
> exist out in space that I decided to delete.

I'm a little confused by this: are you saying that refining with
hydrogens actually added clashes that weren't there before?  To
clarify, when you calculate clashes, either in Phenix, Coot, or the
Molprobity server, this is *always* done with explicit hydrogens,
which is the entire point of the exercise.  So if adding hydrogens is
making the clashes worse, there's something weird going on.*

(* The one exception is that Reduce doesn't always take heteroatoms
into account when adding hydrogens, so it's possible, albeit unusual,
for hydrogens to run into, say, an iron sulfur cluster because they
weren't positioned well.)


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