[phenixbb] Input NCS operators for AutoBuild

Nathaniel Echols nechols at lbl.gov
Wed May 5 09:46:04 PDT 2010

On Wed, May 5, 2010 at 8:40 AM, Mark A Saper <saper at umich.edu> wrote:

> I am having the exact same problem.  I need the NCS parameters in a format
> suitable for AutoBuild which I think is different than phenix.refine.  Are
> you trying to use phenix.simple_ncs_from_pdb routine in GUI?  Let me know if
> you have made any progress.

Actually, I think you have a completely different problem.  Although I
should mention that the GUI program doesn't really deal with the
AutoBuild/RESOLVE output, but the file should still be generated.  I'll try
to make this more versatile - I'm not entirely sure how the differenmt NCS
inputs work, though.

On Tue, May 4, 2010 at 7:54 PM, Mark A Saper <saper at umich.edu> wrote:

> Does anyone know how to generate a custom NCS definition file that
> AutoBuild will read from the refinement format?  The parameter
> is input_ncs_file =
> I used phenix.simple_ncs_from_pdb to generate 3 ncs format files.  But I
> could not figure out how to make the program use my definitions.  In any
> case simple_ncs_from_pdb outputs 3 formats in ./phenix/tmp:
> simple_ncs_from_pdb.ncs
> simple_ncs_from_pdb.ncs_spec
> simple_ncs_from_pdb.resolve
> I tried the last one, but it has no residue or chain specification.  Should
> I use the .ncs_spec?  The first one is for phenix.refine.

I'm not sure what the difference between the .ncs_spec and .resolve files is
- Tom will have to answer this.  However, there are two types of NCS
information which are being confused here, both of which are output by
simple_ncs_from_pdb.  For phenix.refine, it is just atom selections, which
are used to restrain the coordinates and ADPs of individual atoms.  I'm not
sure whether or not phenix.refine applies any of this information directly
to the output maps (Pavel?).  For AutoBuild/RESOLVE, you get NCS operators
(some kind of matrix, I guess), which tell RESOLVE how to incorporate NCS
into density modification.  Conversely, I'm not sure if RESOLVE uses NCS for

If you want to use the NCS information for both density modification and
refinement, you need to supply two files: the input_ncs_file, which will be
the operators for RESOLVE, and a config file for phenix.refine, which will
be the restraint group definitions.  The latter is input for AutoBuild using
the parameter refine_eff_file_list (as the name implies, you can have more
than one).  From the GUI, you can add the phenix.refine config in the main
window as long as the extension is recognized (.eff, .def, .params), but
input_ncs_file is found in the "NCS" dialog window.

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