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

[Haytham Wahba]

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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