# [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...

Pavel.

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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