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

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 ([email protected]) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain 2012/10/9 Nathaniel Echols

On Tue, Oct 9, 2012 at 1:08 AM, Claudia Millán Nebot 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 _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb