Re: [phenixbb] calculating anomalous differences from a model

A related question: is there a current example of using phaser to calculate SAD LLG maps from a refined model not refined with phenix.refine? In the past I have used the description posted here: http://www.phenix-online.org/pipermail/phenixbb/2008-July/012399.html However phaser syntax and keywords seem to have changed a bit as this no longer works. Also, have the derived FLLG and PHLLG columns been renamed ? thanks, Alastair Fyfe On 04/03/2014 09:13 AM, Nathaniel Echols wrote:

PS. Tom pointed out that the anomalous measurability in Xtriage depends on the sigmas, which is obviously a problem for synthetic data - you can generate fake sigmas with "add_sigmas=True", but the resulting statistics will be meaningless.

-Nat

On Thu, Apr 3, 2014 at 8:27 AM, Nathaniel Echols wrote:

...

I guess it depends on what you're looking for as the final output. It's easy to generate an MTZ file with anomalous Fcalc (this is in the GUI too, of course):

phenix.fmodel model.pdb high_resolution=2.0 type=real wavelength=0.9792

Extracting some kind of useful summary from the data might require a little extra scripting - although this may be the kind of thing we should just add to Xtriage (which only reports "anomalous measurability" right now).

-Nat

On Thu, Apr 3, 2014 at 7:20 AM, Jonathan Grimes wrote:

...

Given a refined protein structure, is there an straightforward way to calculate the anomalous differences as a function of resolution, at wavelength X.

many thanks jon

Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer DIAMOND Research Fellow

Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK

Email: [email protected], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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