[phenixbb] help with Histidine flip in phenix refinement
pafonine at lbl.gov
Thu Jan 19 06:11:15 PST 2017
you asked this or very similar question the other day and I replied on
1/7/17, 08:07. Repeating:
set nqh_flips=False or disable real-space refinement. That will stop
flips from happening.
I'd like to address this issue in phenix.refine centrally, so these
unwanted flips do not happen. For this it would be helpful to have an
example. Could you please send me model files before and after
refinement and the data file, and also tell what His flips?
Excluding atoms from refinement:
which is really the last resort.
On 1/19/17 02:36, Vikram Dalal wrote:
> Hi all,
> I have 4 Mn (2 Mn in each chain) in my protein structure. One Mn has
> 1 cordination with water, 1 cordination with His and 4 cordination
> with Asp. I model build the His in coot. Even this His is in bond
> range with Mn. But, when i refine this model in phenix. This His again
> flip other side (N terminal which has to cordinate with Mn goes to
> other direction). I am facing this problem only with His of A chain
> only while N of His of B chain are towards Mn only.
> Is there any option in pehnix refinment where we can exclude a
> specific residue or atom in refinment??
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