[phenixbb] Changing NCS groups

Edward A. Berry BerryE at upstate.edu
Fri Jan 22 22:13:08 PST 2016



On 01/22/2016 05:54 PM, Marie Elizabeth Fraser wrote:
> Hello,
>      I would like to edit the NCS information for a model with two chains.  I've tried running find_ncs and editing the phil file, but I get an error when I try to use my edited file in the next cycle of refinement.  I've tried using the utility to detect NCS groups, then edited in the little windows - also no success.  How are other people defining NCS when they aren't content with the equivalences the program finds?
>      Thank you for your insight,   Marie
>

If you really do want to tweak the NCS restraints manually, and if you want cartesian restraints,
In an ancient version of phenix.refine (dev1745), it used to be possible to specify
in the .eff file with the below syntax (duplicate the blank group which is already present).

I think if you first use auto detection (and cartesion ncs) these lines will be
generated in the output .eff and .def file.
You can then edit them in the .def file and run, perhaps going back to the
original pdb for input in case inappropriate restraints destroyed the output
of that first run. (And turn off find_automatically)

You can look at the .geo file from the first run to find the
biggest violations in your orig pdb, then look at the input and output files
in the density, and decide in each case if it is a true violation that should
be released from NCS.

You can duplicate the restraint_group section as many times as you like in case
you have multiple chains in the monomer or chains that don't behave as a single
rigid body.

refinement {
   ncs {
     restraint_group {
       reference = None
       selection = None
       coordinate_sigma = 0.05
       b_factor_weight = 10
     }
     restraint_group {
       reference = chain A and ((RESID 12:255 and not (resid 205 or resid \
                   184)) or RESID 1001 )
       selection = chain N and ((RESID 12:255 and not (resid 205 or resid \
                   184)) or RESID 1001 )
       coordinate_sigma = 0.05
       b_factor_weight = 0
     }
     restraint_group {
       reference = chain A and ((RESID 256:365 and not (resid 332 or resid \
                   9225)) or ( RESID 1002) )
       selection = chain N and ((RESID 256:365 and not (resid 332 or resid \
                   9225)) or ( RESID 1002) )
       coordinate_sigma = 0.05
       b_factor_weight = 0
     }


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