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

Claudia Millán Nebot cmncri at ibmb.csic.es
Tue Oct 9 05:35:31 PDT 2012

Hi Nat, thanks for pointing it out. Actually, i'm preparing this for a
small example script in order to include it in a practical seminar about
the features and tools of the cctbx, so it is not that critical, but I
would be glad to get some example code of how to use it properly, because
my plans are to deepen into the use of these tools.

Thanks again :)

Claudia Millán (cmncri at ibmb.csic.es)

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain

2012/10/9 Nathaniel Echols <nechols at lbl.gov>

> 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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