Hi Vikram,

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:
http://phenix-online.org/documentation/reference/refinement.html#refinement-of-coordinates
which is really the last resort.

Pavel

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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