Personal tools
You are here: Home → documentation → 2dx Software → Manual → Data Flow → Merging in 2dx_merge in 2D
 

Merging in 2dx_merge in 2D

This processing merges several images into one dataset. This here describes the merging of several non-tilted images into a two-dimensional dataset.




origtiltd

    takes several APH/${imagename}.fou.cor.aph
    generates APH/merge.aph, which now has for each spot potentially many entries
    Filename: APH/merge.aph 
1: Header
2:    H     K     Z*        AMP             PHS             NO    IQ  WEIGHT         BACK         CTF
                            AMP is the raw measured value, not yet changed
                                            PHS is CTF phase flipped, and has also the PhaseOrigin applied to it
                                                                      WEIGHT is .... ToDo

Example:
      1001
      1     0  -0.0000     70.8670        -88.1100           65551 -6  0.078805     47.8734      -0.083
      1     0   0.0000     112.300        -21.6200            6543  6  0.192624     74.5000      -0.093
      1     0   0.0000     25.0594        -131.430           65551  8  0.027867     49.3105      -0.088
      1     0   0.0000     31.3698        -46.4300          665202  8  0.055313     44.8141      -0.094
      1     0  -0.0000     29.1893        -120.570          655302 -8  0.045419     35.9687      -0.096
...
      2     0  -0.0000     120.801        -160.000            6557  4  0.192729     48.7613      -0.165
      2     0  -0.0000     156.540         169.480          665202 -2  0.276022     34.6150      -0.154
      2     0  -0.0000     202.253         170.080          655201 -3  0.375352     51.5399      -0.167
      2     0   0.0000     9.95763         167.980          655502  8  0.013483     37.5852      -0.138
      2     0  -0.0000     102.017         167.300          655502  4  0.138136     42.3687      -0.122
...
      2     0   0.0013     411.287        -178.300            7032  1  0.440457     50.2215      -0.383
      2     0   0.0013     313.198        -178.300            8032  2  0.307053     40.1020      -0.385
      2     0   0.0016     298.834        -161.900            5685  2  0.360523     61.4043      -0.198
      2     0   0.0019     296.552         176.500            6666  2  0.338671     57.6485      -0.250
      2     0   0.0024     330.403        -177.000            8005  1  0.263018     33.6716      -0.509

avramphs:

    uses zminmax = -0.025...0.025, to make sure only non-tilted data participate.
    takes APH/merge.aph
    generates APH/avrg2D.hkl
    Filename: APH/avrg2D.hkl
1: merging number
2:   H     K     L        AMP            PHS             FOM
                          AMP is an average of several spots, and the values are now amplitude-CTF corrected (without inverting the sign).
                                         PHS is an average of several spots, which are already CTF and phaseorigin corrected 
                                                         FOM is calculated as.....ToDo

Example:
      1001
     1     0     0     196.833        -64.0629         96.9797    
     1     1     0     1018.19        -6.10076         99.9556    
     1     2     0     162.905        -177.142         98.7745    
     1     3     0     262.806        -179.891         99.5678    
     1     4     0     123.772        -152.694         97.1893    
...
     2     0     0     453.627        -177.303         99.8751    
     2     1     0     109.832         4.30570         94.4169    
     2     2     0     1278.94         177.975         99.9585    
     2     3     0     288.222         179.579         99.7178    
     2     4     0     382.900        -2.25470         99.9126

centric2.exe:

    takes APH/avrg2D.hkl
    generates APH/centric2D.hkl
    Filename: APH/centric2D.hkl
1: Header
2:   H     K     L        AMP            PHS            FOM

Example:
      1001                                        
     1     2     0     162.905         180.000         98.7745    
     1     3     0     262.806         180.000         99.5678    
     1     4     0     123.772         180.000         88.8569    
     1     5     0     272.380         180.000         99.8588    
     1     6     0     287.654         180.000         99.9085    
...
     2     0     0     453.627         180.000         99.8751    
     2     1     0     109.832         0.00000         94.4169    
     2     2     0     1278.94         180.000         99.9376    
     2     3     0     288.222         180.000         99.7178    
     2     4     0     382.900         0.00000         99.9126

2dx_hklsym.exe:

    takes APH/centric2D.hkl
    generates APH/sym_noheader2D.hkl
    Filename: APH/sym_noheader2D.hkl
1: Header
2:   H     K     L         AMP            PHS            FOM

Example:
     0     2     0     453.627        -180.000         99.8751    
     0    -2     0     453.627         180.000         99.8751    
     0    -2     0     453.627        -180.000         99.8751    
     0     2     0     453.627         180.000         99.8751    
    -2     0     0     453.627        -180.000         99.8751    
     2     0     0     453.627         180.000         99.8751    
     2     0     0     453.627        -180.000         99.8751    
    -2     0     0     453.627         180.000         99.8751    
     0     3     0     350.611         0.00000         99.5364    
     0    -3     0     350.611        -0.00000         99.5364    
     0    -3     0     350.611         0.00000         99.5364    
     0     3     0     350.611        -0.00000         99.5364

sort:

    takes APH/sym_noheader2D.hkl
    generates APH/sym_sort2D.hkl


2dx_hklclean.exe:

    takes APH/sym_sort2D.hkl
    generates APH/sym2D.hkl
    Filename: APH/sym2D.hkl
1: Header
2:   H     K     L         AMP            PHS            FOM

Example:
     0     2     0     453.627         180.000         99.8800    
     0     3     0     350.611         0.00000         99.5400    
     0     4     0     523.815         0.00000         99.9000    
     0     5     0     839.137         180.000         99.9500    
     0     6     0     673.367         180.000         99.9500    
...
     2     0     0     453.627         180.000         99.8800    
     2     1     0     109.832         0.00000         94.4200    
     2     2     0     1278.94         180.000         99.9400    
     2     3     0     288.222         180.000         99.7200    
     2     4     0     382.900         0.00000         99.9100

f2mtz.exe:

    takes APH/sym2D.hkl
    generates merge2D.mtz
    Filename: merge2D.mtz
SYMMETRY ${CCP4_SYM}
LABOUT H K L F PHI FOM
CTYPOUT H H H F P W
Document Actions

I don't understand

Posted by Michael Matho at Jun 16, 2009 08:10 PM
I'm sorry but this is not clear at all. Is this a tutorial or something for more advanced users? A step by step sequential explanation (with actual images of the GUI) would be very helpful! Thanks, Michael.

Not a tutorial, but a cheat sheet

Posted by Henning Stahlberg at Jul 10, 2009 09:00 AM
Dear Michael,

2dx and the underlying MRC programs process and then evaluate images, and extract values for amplitudes and phases of Fourier spots. These are then handed over from one program to the next one, where each program does something to those values (e.g. correcting for the CTF, or merging several values together). Each program thereby unfortunately needs a different type of data that is therefore often in a different format, and the whole thing quickly gets very confusing. Most of these files are text files (ASCII), though, so that you can always open them with a text browser (vi, edit, SimpleText, or even Word (but don't save it back as "Word" file.doc file). We have here compiled a list of all the programs that are called in sequential order, and have listed the input and output files for these programs. For the output files we have then included a short description of the file format, followed by an example of how that should look like. This is only for reference purposes, in case somebody tries to follow the flow of data from one program to the next one.

Henning
« February 2012 »
February
MoTuWeThFrSaSu
12345
6789101112
13141516171819
20212223242526
272829