[phenixbb] Disappearing density?

Tom Terwilliger terwilliger at lanl.gov
Tue Aug 10 08:32:51 PDT 2010

Hi Pavel,

I haven't thought about it a lot, but here is my understanding of the  
effect.  A symmetry axis (e.g., 2-fold) basically is the same as  
having 2 identical cells on top of each other, rotated 180 degrees.  
Imagine that cell 1 has random density.  Then cell 2 has the same  
random density, rotated 180 degrees. Now add them together. At most  
points, the density from cell 1 and cell 2 are different, and the RMS  
of their sum is about sqrt(2) times the RMS of either one.  On the  
other hand, at the symmetry axis, the density from cell 1 and cell 2  
are identical, so that they always add constructively and the RMS is 2  
times the RMS of either one.  As you move away from the axis, the  
effect is smaller, and it decays away over the resolution of the map.   
Note that if you have a 3-fold, 4-fold or 6-fold, then the effect is  
even bigger.

All the best,
Tom T

On Aug 10, 2010, at 9:07 AM, Pavel Afonine wrote:

> Hi Tom,
> On 8/10/10 7:36 AM, Tom Terwilliger wrote:
>> 1. Yes, it is possible that the presence of a symmetry element very  
>> near the problematic area can make the density noisier. Normally  
>> this happens only right at the symmetry element however, not even a  
>> few A away.
> could you please explain why this happens?
> Thanks!
> Pavel.
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
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