[phenixbb] To evalute the LLG value by given the structure factor information only

Pavel Afonine pafonine at lbl.gov
Sat Apr 30 23:53:11 PDT 2011

Hi Hailiang,

> Yes, I understand it is part of phenix.refine output, but I am wondering
> whether there is a way to evaluate LLG by only using user-provided
> structure factor (Fo, sigFo, Fc).

internally in PHENIX there are many pieces of code that do this (like 
X-ray target calculation in phenix.refine), but I am not aware of any 
dedicated program that is exposed to the end-user and that does this. So 
I guess the quick answer is "no". If you think it is important to have 
then, as I mentioned before, I can and add it to phenix.model_vs_data 

> I think phenix.refine will have to read
> a PDB file, based on which model Fc will be calculated and used to
> evaluate LLG (instead of my provided Fc).

This is true. It will have to read a PDB file to obtain Fmodel (which is 
not just Fc).

> I know there is a well-established LLG formula and may write a short code
> but I need to minimize sigmaA I think which take some efforts:-(

Not sure the code will be short since you have to estimate sigmaA (or 
alpha/beta - what's used on phenix.refine). By the way, in this case 
your input will also have to include free-R flags in addition to Fo and 
Fmodel. I recall I spent more than a week before I got it right and fast -;)


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