This is an option only useful to crystallographers.
A crystallographer often wanders if something strange
is going on with the reflections.
The option CHKMDF allows for a visual inspection of a set of reflections.
The reflections should be stored in the form of an MDF.
One can read up to four columns from such a
file, and put a subset of the reflections, coloured as function of any
property, at the screen. These
reflections can be picked if wanted.
When working with MDF's one should keep a few things in mind. The first thing
is that WHAT IF internally generates column 0. This is the column in which
WHAT IF works. If you type LSTMDF you get a listing of all relections that are
read from the MDF. In this list you will see the miller indices, the (maximally
four) columns you read in, and the internal column zero. This column
contains column worked on after an option that works on one column, the
difference of the two columns in case of the usage of an option that uses
such a difference, etc. WHAT IF then holds internally two extra columns, one
column is called the trigger column. If this column is set to true, the
reflection will be used the next time all reflections are sent to the screen.
The last column is the colour column. Whenever you use any of the COL***
options, this column will (partly) be overwritten. So the command GRAMDF
will send one dot to the screen for every reflection in the MDF for which the
trigger is true, in the colour as set in the colour column.
WHAT IF allows you to give general commands, colouring commands, and triggering
commands from the CHKMDF menu.
If something strange happens, you migth try one of the following things:
Read the columns in in a different order.
Try to read the first column of the MDF as the first column for WHAT IF.
The command GETMDF will cause WHAT IF to prompt you for a file name. Be aware
that the program might crash if the file you give is not an MDF. It will
thereafter promt you for a resolution limit. This is the highest resolution
that will be read from the MDF. WHAT IF generates all possible reflections
up to that resolution. If the reflection is not found in the MDF, it will
be marked by WHAT IF as absent. Finally you will be prompted for the column
number(s). You can give up to four column numbers to be read. Thereafter you
can work only with these columns, although you can of course always read the
MDF again, and then take other columns.
In case of strange errors, try reading the MDF with a lower resolution limit.
WHAT IF can only hold 32000 (?) reflections, and does not check for overflow.
The command GRAMDF will send all reflections for which the trigger is set
to TRUE to the graphics screen.
They will get the colour last given to them with
one of the COL*** options. You will be promted for the number of the
mol-object, and the name of the mol-item.
The command DIFSTS will cause WHAT IF to prompt you for two columns. For
every reflection present in both columns the difference (value in second
column) - (value in first column) will be calculated. Thereafter the
average difference, the mean linear deviation from the average, the mean
quadratic deviation from the average (=standard deviation), the mean third
power of the deviation from the average (=skewness), and the mean fourth
power of the deviation of the average (=curtosis) and the variance will
be calculated, and printed. See chapter 13 of 'Numerical Recipes'.
The command WILSON will cause WHAT IF to prompt you for a column number. A
Wilson plot will be generated for the data in this column. You will be
prompted for a mol-object number, and a mol-item name, and the Wilson
plot will show up at the screen.
After the command COLALL you will be promted for a colour. Give, as usual,
a number between 1 and 360. All reflections will now get this colour. Be
aware that reflections already send to the graphics window earlier
will keep their colour at the
screen, but they will get the new colour the next time they are displayed.
The command COLSIZ will cause WHAT IF to prompt you for a column number, a
colour, and a size range. It will then colour all reflections in the given
column that have their value in the given range as requested. If you give
only one value when the range is requested, all reflections larger than that
value will be coloured. Also those with value 1E10.
The command COLDIF will cause WHAT IF to prompt you for two columns. It will
then calculate the difference (value of second column) - (value of first
column). You will thereafter be promted for a range and a colour. All
calculated differences that fall within the given range will get the
requested colour.
The command COLABS will cause WHAT IF to prompt you for a column number, and the
colour for present and the colour for absent reflections. All reflections
will be coloured as function of their absence or presence in the requested
column.
If you want to change the default bin ranges that WHAT IF uses in the COLBIN
option, you can use SETBIN. WHAT IF will then first show the present bins,
and then prompt you for the new bin boundaries. You should give AT LEAST TWO
numbers. All bin boundaries should be type on one line, separated by comma's or
by blanks. The bins will be coloured from 0 (=blue) to 200 (=yellowish green)
in equal steps.
The command TRGALL will switch the trigger on for all reflections. That means
that the next time you send the reflections to the graphics window
(with the GRAMDF
command) all reflections will be shown.
The command TRGSIZ will cause WHAT IF to prompt you for a column number
and a size range. It will then switch the trigger on for all reflections
in the given
column that have their value in the given range. If you give
only one value when the range is requested, all reflections larger than that
value will be switched on. Also those with value 1E10.
If you want to switch on or off a block of reflections limited by h, k, and l
boundaries, you should use the option TRGHKL. You will be promted for
the limits on h, the limits on k, and the limits on l. Thereafter you will be
ask if you want to switch them on. If you answer YES, the requested block
of reflections will all be switched on. If you answer NO, they will be
switched off. If you want to see just one plate of reflections (eg. h=0),
you can give the values 0,0 if promted for the limits on h.
The command TRGRES allows you to switch reflections on or off as function
of their resolution. WHAT IF will prompt you for a resolution range (in
Angstroms), and it will ask you whether you want to switch this range on. If
you answer this question wit YES the requested range will be switched on. If
you give NO, the requested range will be switched off.
The command TRGDIF will cause WHAT IF to prompt you for two columns. It will
then calculate the difference (value of second column) - (value of first
column). You will thereafter be promted for a range. All
calculated differences that fall within the given range will get the ir trigger
switched on.
The command TRGABS will cause WHAT IF to prompt you for a column number. It
will then ask if you want to switch the present reflection on. If you say
YES then all present reflections will be switched on, and the absent reflections
will be switched off. If you answer NO, this will be done the other way
around.