[cctbxbb] Going from a pdb file to an x_ray_structure object

Nathaniel Echols nechols at lbl.gov
Tue Oct 9 05:12:28 PDT 2012


On Tue, Oct 9, 2012 at 1:08 AM, Claudia Millán Nebot
<cmncri at ibmb.csic.es> wrote:
> i'm trying to get an xray.structure object from a pdb file, as i'm
> interested on using both this and a Miller array coming from a reflection
> file to calculate correlation coefficients between Fobs and Fcalc.

I'm glad you were able to figure this out from the examples, but I
have one caveat about your goal: if you're working with
macromolecules, the Fcalc you get from an xray.structure object is
going to be suboptimal because it won't contain any contribution from
bulk solvent - only the point scatterers in the PDB file will be
included.  It may be necessary to use the (much messier) mmtbx.f_model
API, which incorporates the bulk solvent (and also scales Fobs and
Fcalc, although this isn't actually necessary for simple CCs).  This
isn't as well documented but I can give you some template code if you
need it.

-Nat


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