[phenixbb] calculating anomalous differences from a model

Alastair Fyfe afyfe at soe.ucsc.edu
Thu Apr 3 09:28:31 PDT 2014


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 <nechols at lbl.gov> 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 <jonathan at strubi.ox.ac.uk>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: Jonathan at strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk
>>> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>
>
>
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