[phenixbb] Disappearing density?

Pavel Afonine pafonine at lbl.gov
Tue Aug 10 09:13:00 PDT 2010

  Hi Tom,

thanks! Interesting... I wonder if we need to correct Fo-Fc maps for 
this effect since a few such peaks (especially large ones in case of 
high order symmetry) may make a weak ligand density even less visible...


On 8/10/10 8:32 AM, Tom Terwilliger wrote:
> 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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