[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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