[phenixbb] Question about scale of ED maps from phenix vs map coeffs when displayed in COOT

Pavel Afonine PAfonine at lbl.gov
Sat Mar 21 21:38:47 PDT 2009

Hi Dale,

this was one of my suspicions... Since Coot computes maps dynamically in 
a box around the point you click on, I was thinking that it normalizes 
the map in that box and not in whole unit cell, therefore the 
difference. I don't know, just a guess. It would be helpful if Paul E. 
could comment on this...


On 3/21/09 8:11 PM, Ralf W. Grosse-Kunstleve wrote:
> For phenix maps: the sum is over the entire unit cell.
> Ralf
>>     Is the sum over the asymmetric unit or the portion of space that
>> happened to be covered by the map?  The result of this calculation
>> depends greatly on the amount of solvent region that is included in
>> the sum.
>> Dale Tronrud
>> Ralf W. Grosse-Kunstleve wrote:
>>>> That was (and is) always a mystery for me: when I look at two maps (both 
>>>> coming from phenix.refine):
>>>> - one is computed in COOT from phenix.refine map coefficients, and
>>>> - another one displayed in PyMol using X-plor formatted map.
>>>> To make both maps looking identical I have to draw them at different 
>>>> sigma levels, sometime very different. This is true for both fo-fc and 
>>>> 2fo-fc maps.
>>>> I have some ideas but no any proofs so I don't want to put my 
>>>> speculations to the bb. So, I have no answer... May be Ralf or Paul E...?
>>> Our "sigmas scaled maps" are simply divided by the "biased standard
>>> deviation":
>>>       sqrt(sum((value-mean)**2) / n)
>>> The mean of our maps is usually zero, as we don't usually include F000.
>>> Ralf
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