Empirically, you can leave out a couple of "average" atoms in the
structure, and recalculate the maps. If you leave out a O, N, and C atom,
with relatively average B's, then you know how many electrons you should
be seeing for each in the difference map. Note that the peak height will
vary due to errors in phasing or B-factor.
Bernie Santarsiero
On Mon, April 20, 2009 11:18 am, Pavel Afonine wrote:
> Hi Thiyagarajan,
>
> the latest version of PHENIX has a command line tool called
> "phenix.real_space_correlation", that for each atom or residue computes:
>
> - map CC (where a user can define any map types, the default: 2mFo-DFc
> and Fc maps),
> - 2mFo-DFc map value at atom center,
> - mFo-DFc map value at atom center.
>
> Please let me know if you have question,
> Pavel.
>
>
> On 4/20/09 3:47 AM, S. Thiyagarajan wrote:
>> Dear CCP4 users
>>
>> Is there any easy way of calculating the peak height / number of
>> electrons at a given position, say a mouse click point in coot.
>>
>> Is there any formula to calculate the number of electrons based on
>> sigma level and peak height, as given in difference map peaks in coot.
>>
>> I have some peaks in my map which take water or sodium/magnesium or
>> chlorine atom with out giving out any positive or negative density
>> upon further refinement.
>>
>> The asymmetric unit has about 425 residues and the data resolution is
>> 1.5A.
>>
>> Thanks and regards
>>
>> S. Thiyagarajan
>> Department of Cell and Organism Biology
>> Lund University
>> Sölvegatan 35
>> Lund, Sweden
>>
>>
>
|