[phenixbb] is there any phenix utility that can evaluate the Patterson Correlation function between exp and model data?

Randy Read rjr27 at cam.ac.uk
Tue Jun 21 00:45:04 PDT 2011


Is there a particular reason you want to use PC refinement?  In most cases I think it is better to refine against a likelihood target.  I think Frank used it in Rosetta for speed, which is more important when you have hundreds or thousands of trials.

Regards,

Randy Read

On 20 Jun 2011, at 19:02, zhangh1 at umbc.edu wrote:

> Yes, this is a coarse-grained model structure factor, and I want to refine
> it against Patterson correlation with the exp data.
> 
> If there is no direct syntax, any suggestions about which module/file in
> the phenix package I should look for will be greatly appreciated!
> 
> Best Regards, Hailiang
> 
>> In theory one may have a non-atomic model, say a 3D function defining
>> the molecular envelop or some other non-atomic representations (Kalinin,
>> D. I. (1981). Kristallographiya, 25, 535-544.). Fourier transforming
>> these objects will give you the model structure factors F.
>> 
>> Pavel.
>> 
>> 
>> On 6/20/11 9:53 AM, Jacob Keller wrote:
>>> I am curious--how did you get model F's without the coordinates?
>>> 
>>> JPK
>>> 
>>> On Mon, Jun 20, 2011 at 9:52 AM,<zhangh1 at umbc.edu>  wrote:
>>>> Hi,
>>>> 
>>>> If I only have the experimental and model scattering factors (without
>>>> model coordinates), is there any phenix utility that can evaluate the
>>>> Patterson Correlation function between exp and model data?
>>>> 
>>>> By the way, is the one by FFT as described in
>>>> (http://www.nature.com/nature/journal/v473/n7348/full/nature09964.html)
>>>> implemented in Phenix?
>>>> 
>>>> Thanks a lot!
>>>> 
>>>> Hailiang
>>>> 
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>>> 
>>> 
>> 
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> 
> 
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------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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