A missing number flag (MNF) will indicate that a certain datum for an HKL record has not been measured or calculated. This means that any datum within an MTZ can be tested to see if it should be used. Previously files did not contain this information for all data types. There was only one way of distinguishing an unmeasured reflection and that was by checking if its standard error SIGF or SIGI was zero. It was possible to test if an experimentally determined phase had been calculated by checking if its FOM was zero.
Example 1)
A list of reflection data from one crystal would contain only
those values of hkl which had an observation associated with them.
E.g. If you had a blind region up the C* axis for a P212121 data set:
your file might begin
0 0 8 F SIGF
0 0 10 F SIGF
.....
from which you could deduce that there was no measurement made for
reflections 0 0 2, 0 0 4, and 0 0 6
Example 2)
For an MTZ file containing native and derivative data sets.
an old style MTZ file could look like this:
H K L FO SIGFO FPH SIGFPH FOM PHIB FreeRflag
0 0 6 0 0 40 4 0.00 0.0 9.0
0 0 8 10 1 0 0 0.0 0.0 1.0
0 0 10 75 2 80 5 0.25 45.0 9.0
...........
From this you could deduce that there was no measurement made for 0 0 8
for the derivative FPH, no measurement of FP for 0 0 6, no measurement
for either FP or FPH for 0 0 2 or 0 0 4. and therefore no phase or FOM
could be calculated for these reflections.
It was possible to mis-use these old-style files by assigning F without assigning SIGF or PHI without FOM. Many people have done "difference" maps where some "differences" were between observed and unobserved data, and where phases were taken as 0.00 when in fact no phase had been determined.
In the new style MTZ file the missing number flag (MNF) will indicate a datum is not present.
Example 1) would appear as
0 0 2 MNF MNF FreeRflag
0 0 4 MNF MNF FreeRflag
0 0 6 MNF MNF FreeRflag
0 0 8 F SIGF FreeRflag
0 0 10 F SIGF FreeRflag
Example 2) would appear as
0 0 2 MNF MNF MNF MNF MNF MNF 6.0
0 0 4 MNF MNF MNF MNF MNF MNF 3.0
0 0 6 MNF MNF 40 4 MNF MNF 9.0
0 0 8 10 1 MNF MNF MNF MNF 1.0
0 0 10 75 2 80 5 0.25 45.0 9.0
All CCP4 programs that use MTZ files have been changed in order to deal with MNFs. No program will use a datum flagged with a MNF. The functionality in most cases has remained the same and also to ensure backwards compatibility the old style checks on SIGF and FOM have still been kept where appropriate.
It is strongly advised that you should change existing MTZ file to the new style MTZ format. This is possible through MTZMNF, a new program in the Suite . It uses the old protocols for checking for missing data and then replaces them with MNF. (see mtzmnf.doc)
Existing programs which output data, such as MLPHARE, will now output MNF for undetermined phase and FOMs. Therefore, if the input file to MLPHARE is an old style MTZ file, the output will be a hybrid of both old and new. This is undesirable.
There is now an option in FFT that will allow you to substitute Fc for "nFo - (n-1)Fc" as the Fourier term for all missing values of Fo (see fft.doc). This invokes the assumption that the most likely value for Fo is Fc. REFMAC ( and soon SIGMAA) will generate a term DFc to substute for 2mFo-DFc. This reduces the distortion caused by missing slabs of data. Although the noise in the map will diminish, it is possible that the systematic error (model bias) may increase. Note, that this substitution is not needed for difference maps (Fo-Fc) where the assumption Fo~Fc will generate a zero difference.