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

amadrona at uci.edu amadrona at uci.edu
Thu Aug 19 15:46:34 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.*
>No, I didn't previously have hydgrogens.  This is the first time I looked
at close contacts with hydrogens present.  I submitted my pdb to the the
PDB auto Deposition input tool which defines "close contacts" as less
then 2.2 A
After looking at these I could see that many were between hydroens of one
side chain and usually an amid or sometimes CA of the mainchain. 
Sometimes they appeard hydrogen bonded but the hydrogens had to be rotated
away.  All I had to do was rotate the hydrogens.  I was just suprised that
this would not have been done in automatically in the refinement.

(* 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.)
> -Nat
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