[phenixbb] sca file & anomalous difference map: understanding the story from the scratch,

[Thomas C. Terwilliger]

Hi Haytham,

It is important to differentiate between "unmerged" and "anomalous":

unmerged means "each measurement of each reflection kept with the original
indices"
merged means "measurements mapped to the unique set and averaged"

anomalous means "keep Bijvoet pairs separate, consider them separate
reflections"
non-anomalous means "consider Bijvoet pairs as repeat measurements of the
same reflection"

So your first data file is "merged" and is "anomalous". Your second I
can't tell for sure but if you have anomalous off, it is probably merged
non-anomalous.

So for your anomalous difference map you can use a merged or an unmerged
file, but it must be anomalous data.

I hope that helps!
-Tom T


>> i am new user
>>
>> first Q??
>> with HKL2000 (with scale anomalous option: ON)
>>
>> the output.sca file is like that (for example):
>>   1
>>  -985
>>     38.064    89.066    51.543    90.000   100.446    90.000
>> p21            
>>    0   0   2  3433.6    77.1
>>    0   0   3   735.6    14.0
>>    0   0  11  1564.7    25.4
>>    0   0  12  5643.2    88.3
>>    0   0  13   541.5     9.7
>>    0   0  14  1701.0    27.4
>>    0   1   1  2060.5    47.0
>>    0   1   2  4115.3    75.3   4257.1    97.5
>>    0   1   3  8782.0   280.6  7728.9   173.9
>>    0   1   5  1760.8    28.4  1778.5    33.5
>>    0   1   6  6650.2   122.2  6843.2   126.0
>>    0   1   7  1935.8    36.6  1794.2    29.1
>>  
>> is that one is merged or unmerged?????
>>
>> if i compare with the output.sca with scale anomalous option (off):
>>    0   0   2  3444.4    77.3
>>    0   0   3   734.9    14.0
>>    0   0   4  1705.0    27.5
>>    0   0   5  2693.8    49.4
>>    0   0   6  8383.1   153.9
>> -------------------------------------------------------
>> second Q?
>> using output.sca (with scale anomalous option on) for molecular Replacment
>> generate MR.mtz
>> which shows F,SIGF in data labels under phenix.refine
>>
>> the generated (refine_data.mtz) shows:
>> I-obs(+),SIGI-obs(+),I-obs(-),SIGI-obs(-)
>>
>> what is going on in first and second run?
>> -----------------------------------------------------------------
>> third Q?
>> i want to generate anomalous difference map using phenix.map
>>
>> but when i use output.sca (with scale anomalous option: ON) as reflections
>> file
>> the data label show ((i-obs,sigma))
>>
>> how to convert this SCA file (if it is merged) to unmerged sca file to
>> creat anomalous difference map for protein contains Br, Sn and Sulpher??
>> i want to see peaks for these 3 elements to confirm their presence.
>>
>> N.B: the wavelenght was 1.00900
>> N.B: resolution 1.78 A
>> N.B: i use GUI phenix
>>
>> i am sorry for that long e-mail.
>> thank you in advance
>>
>> haytham wahba
>> biochemi
>> UdeM
>> Canada
>>
>>
>>
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