Whenever you are promted for the name of a MOL-item, WHAT IF creates not only
this MOL-item at the screen, but also a file with this name
and the extension .WPL. These files can later be used for many purposes.
One of the possibilities is plotting.
The fact that plotting items is done by using the item files on disk
and not the actual items in the graphics device means that it is also
possible to make plots without a graphics device being present.
WARNING: Lines that have one of their end-points outside the field of view,
will be entirely deleted from the plot, rather than plotted partly.
You can write general plot files with the command PLOT and postscript files
with commands that have PS as part of their name.
The default plot device for WHAT if is a postscript laser writer. This default
has been chosen for the very simple reason that that is what I have available.
If you have a laser printer available somewhere, that can deal with
postscript files, you can use the commands with PS in their name.
The commands to send a plotfile to a colour or black-and-white laserwriter
are located in the CCONFI.FIG file in the dbdata directory. These commands
have to be provided upon initialisation, but can be modified later if required.
If you type PLOT, you will repeatedly be prompted
for mol-item names. WHAT IF will generate a FRODO-style plot file with the
contents of these mol-items in it. You can use the program FROPLO to plot
these items at the HP plotter (this is specific for Groningen. Other sites
should modify this program for their own plot facility). The view, translate,
rotate, scale and slab values that are in use at the moment
you give the PLOT command will be used for all MOL-items in this plot.
Mol-items do not need to be present at the screen in order to be plotted,
because they are read from the files with the extension .WPL.
If you have a laser printer available somewhere, that can deal with
postscript files, you can use the command PSTPLT. This command will just like
the PLOT command prompt you for MOL-items. The only difference is that they
are immediately written in a postscript file. If you have the command to submit
a file to the postscript plotter set correctly in the CCONFI.FIG file,
then WHAT IF wil automatically submit the postscript file
called PLOTR.*** (in case of stereo also PLOTL.*** *** numbers from 101
upwards) to that queue. You
will be prompted for the pen-thickness (=line-width) and line type for each item.
You will have to experiment
with this a little, but 0.5 till 2.0 seem reasonable values for pen-thickness.
Linetype 0 will create solid lines, whereas 1 till nine will create
dashed lines; 1 and 2 seem the best values to use. The plot you get
is the exact copy of what you see of that item
at the screen of the given items, with the exception
that lines that are partly within and partly outside the field of view
will be skipped entirely. See the LINTYP parameter description in the
plot parameter chapter below for automatic line type parameter setting.
If you answer the question "stereo?" with YES, you will an extra plot.
The first plot will be identical to a mono plot. The second plot will
be rotated around the vertical axis by 6 degrees.
You get the question `do you want to
plot the labels (y/n)`. Giving YES will cause WHAT IF to also plot the
pick labels (those are the labels that remain readable when you rotate).
You will be prompted for a title. This title will be plotted on top of
every plot, with as last character R or L for Left or Right plot.
Also the most essential view parameters will be plotted.
The last question is "Plot it Y/N". Answering Y will cause WHAT IF to send
the plot to the laser writer, and to write the plots as postscript files on
disk. Answering N will cause WHAT IF to only write the postscript plot files
to disk.
WARNING. If you want to make plots, then the screen should show a MONO picture,
both when making mono, and when making stereo plots!
The command PSTCPK will cause WHAT IF to prompt you for a residue range.
You can now give any range that contains less than 250 atoms. You
first have put this same range in a mol-item at the screen, because after
the range is given you get some time to set the view at the screen as
desired. Thereafter you only get the question "do you want stereo" to
answer. Take care that the range you are going to plot does not fill the
screen completely, but for only 2/3-th. The postscript plot file will
automatically be submitted to the appropriate queue if the postscript logical
has been set as discussed in a previous chapter.
This CPK plot is not very nice, but at least it is better than nothing.
The command PSVIEW will show you the present viewing matrix of the PS300.
Also related parameters like slab, scale etc. will be displayed.
The command SAVMAT will cause WHAT IF to write the present PS300 view matrix
in a file. A file name will be suggested, but you can choose whatever name
you want.
The command RESMAT will restore a previously saved view matrix. At present
there is no use for this option.
The command USEMAT will set a flag. After this command WHAT IF will with
every next PSTPLT command prompt you for a view matrix file. This should
be either a previously stored view matrix, or a user generated file with
the same format. It is not possible to switch this flag off.
The command PARAMS will, as usual, bring you in the parameter menu. The
following plot parameter can be changed:
The parameter LINTYP has two allowed values: 0 and 1.
The value 0 means that the user is prompted with every mol-item for
a dash parameter and a linewidth. This item is then in its entirity
written to the plot file with the requested dashing and linewidth parameters.
If LINTYP is set to 1, the user is not asked for the dash and linewidth
parameters, but rather these are set differently for every colour. The
relation between the parameters and the colour is read from a file.
The user can provide such a file. If not, the default file is taken.
This fiel should be called LINTYP.FIL, and should be present in the directory
where you are presently working. The format of the file is 36 lines
with each 5 integers I5 on them. The first line is used for all colours
between 1 and 10, the second for the colour bin 11-20, etc. The four
integers have the following meaning:
The first three are the three parameters used by the postscript command
setdash. See the postscript writeup for their meaning; where possible,
the value 0 means absent.
The fourth parameter is the preferred linewidth in units of 1/10-th of a
millimeter. This fourth parameter should normally be chosen between 0.4
and 2.5.