The best way to use MolScript is to work on an SGI IRIS-4D machine (or a
similar system with a program like xpsview and a windowing system). One
window should contain the input file within an editor, and another window is
used to run MolScript and xpsview to display the results. Edit the input
file, save it, run molscript, run xpsview, edit the input file, and so on.
Start with the simplest possible plot (read coordinates, centre all atoms, output CA trace), and work iteratively to orient the molecule properly. Schematic objects (strand, helix, coil, turn) can be put in at an early stage (use Kabsch & Sander's DSSP program to get the secondary structure assignments, if these are not available directly) and may actually be easier to work with from the start.
Only when a good view has been found is it worthwhile to start the fine tuning: setting slab (to get depth-cueing of coil radius), changing colours and shading, drawing CPK or ball-and-stick, adding labels. In particular the fine tuning of labels (depth cueing, size, position, centering, offset) is very dependent on the orientation being set once and for all.
Colour and shading fine tuning is dependent on exactly what kind of output device you will be using (see below: Colour specifications).
Jane Richardson has listed some general points on how schematic drawings of proteins should look (Richardson 1985). Look at her drawings to get inspiration and guidance (Richardson 1981, 1985).
A point that the author would like to make is that 90 degree views of a
structure, if carefully selected, can be very instructive. In fact, such
views can often bring home the message better than stereo plots. With
MolScript, 90 degree views are ridiculously easy to prepare. Stereo plots,
however, are trickier to make (see below).
When displaying superpositions of structures (for instance, sets of structures derived from NMR data), then the 'store-matrix' and 'recall-matrix' commands must be used, rather than the ordinary ways of getting a good view. The reason is that if the 'position' command is used, this will give a slightly different transformation for different coordinate sets, thus destroying the least-squares fit that (almost certainly) has been done previously using some other program. In the display of superimposed NMR structures, this will give plots where it looks as if the structures fit better at the center of the plot than they actually should. The use of 'store-matrix' after the first coordinate set has been transformed, and 'recall-matrix' for the other coordinate sets, ensures that the original least-squares fit is kept intact.
! -- This is a minimal MolScript input file; this line is a comment.
plot
read mol "protein.pdb"; ! Read the coordinate file.
transform atom * ! Xform all atoms so that the centre-
by centre position atom *; ! of-gravity is placed at origin.
trace amino-acids; ! Output a CA trace of the chain.
end_plot
! -- Here the minimal input file ends.
A number of example input files called '*.in' are part of the distribution. These show some examples of what can be done. The makefile can be used to run these examples.