[phenixbb] Changing NCS groups

Pavel Afonine pafonine at lbl.gov
Sat Jan 23 00:05:31 PST 2016


You can have NCS related groups defined automatically or manually for 
restraints (torsion or Cartesian) or constraints, in current version.
Pavel

On 1/22/16 22:13, Edward A. Berry wrote:
>
>
> 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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