[phenixbb] adp values

Pavel Afonine pafonine at lbl.gov
Tue Jan 25 10:21:35 PST 2011

  Hi Agnieszka,

I just replied to similar questions (see Re: [phenixbb] ADP: fix_wxu and 
wxu_scale): all applies here too.

There can be lots of reasons for what you observe, and I think it will 
be inefficient if I start writing pages of text guessing. Alternatively, 
if you send me the data and model then I will have a look and may be 
find out what's happening in your specific case (if you decide to send 
the files please do so to my email address - not to the whole list).


On 1/24/11 8:30 AM, Agnieszka wrote:
> Hello,
> I have 1.96 resolution structure (RNA) which I refine with individual 
> adp factors. I found that in some cases the differences of apd between 
> the covalently bonded atoms is quite large, for example: phosphate 24 
> and one of the oxygen 33; O4' - 26 and C1'-18. In extreme case for the 
> so4 anion is: sulphate atom 63 and one of the oxygen 31. Why is it 
> happened? I was trying refmac and the b-factors are totally different 
> (they are much bigger). Is it because of scaling and resolution?
> thank you in advance,
> Agnieszka Kiliszek

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