[phenixbb] real space correlation

Abhinav Kumar abhinavk at slac.stanford.edu
Tue Aug 21 10:00:31 PDT 2012

Thanks Pavel.

(650) 926-2992

On 08/21/2012 09:48 AM, Pavel Afonine wrote:
> Hi Abhinav,
>> When does it write CC per atom vs per residue? Can you please elaborate?
> it's resolution dependent.
> Say you are looking at ARG (or something similar with long side 
> chain), which has a few atoms sticking out of density, while the other 
> atoms are well placed into density. Then if you compute CC for the 
> whole residue it will still be high enough to mislead you thinking 
> that everything is all right with this residue. However, if you 
> compute CC per atom it will immediately red-flag these few atoms that 
> are not in density.
> Computing CC per atom actually makes only sense if density shows you 
> atoms, that is the data resolution is high enough. For example, you 
> would not want to compute CC per atom at resolutions like 3A or so.
>> Is there a way to tell the program to write CC one way or the other?
> phenix.real_space_correlation allows more fine tuning. In particular 
> it allows you to specify whether to output CC per atom or per residue.
> Pavel

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