mspp file.mspp
mspp file.mspp > file.in ; mscript ... file.in
mspp file.mspp > file.in ; molscript ... file.in
mspp file.mspp | molscript ...
NOTE: mspp can only be run on zinc and cobalt at this time.
mspp takes an input file with a much simpler syntax (see below) and produces a Molscript format file from it.
mspp supports nearly all of the graphics commands (e.g. helix, ball-and-stick) and parameters (e.g. residuecolour, transparency) that are found in Molscript using the same names. In particular the graphics commands that are supported are those that draw portions of the molecule (helix, bonds, cpk, ...), but not the more obscure commands that draw non-molecular objects (label, object, pointlight, ...).
Also currently unsupported are the header commands and transformation commands, except that a center command not found in Molscript has been provided to center all atoms.
As mentioned above, the names of the commands and parameters in mspp are exactly the same as those in Molscript.
The format for atom and residue specification is the same as what
is used in Midas. That is, residues are given in the form:
:num1 :num1,num2 :num1-num2 etc.
Atoms are specified in the form:
@atom1 @atom1,atom2 etc.
Note, however, that the interpretation of the atom names is performed by Molscript. In Midas, the backbone atoms would be specified as @n,c,ca but Molscript insists on the atoms having the same capitalization as in the pdb file, thus the backbone atoms would have to be specified in mspp as @N,C,CA. Also, Midas uses "=" as a wildcard for atoms, with "c=" representing all carbon atoms. Molscript, however uses "*" as the wildcard and all carbons would be "C*".
Colors may be specified according to their Molscript names ("red", "blue", "gray 0.7", etc.) as a Molscript style rgb or hsb specification ("rgb 0.3 0.4 0.5") or simply as a triplet of numbers ("0.2 0.3 0.4") which will default to rgb (as opposed to hsb) colorspace. If you don't know what hsb colors are, ignore them.
Commands go until the end of the line unless terminated by a semicolon ";". This allows the normal usage of one command per line, but also permits multiple commands on a single line if needed.
Below is an example that will demonstrate many of the above concepts. It will draw a red helix and dark gray beta-strand connected by a blue-gray coil. In addition to the backbone, the carbon sidechains of several residues are drawn with purple ball-and-stick, and a transparent surface is drawn in blue for six residues.
read test.pdb center colourparts on atomcolour :8-15 purple residuecolour :1-10 red residuecolour :11-20 0.4 0.5 0.2 residuecolour :21-40 gray 0.4 helix :1-10 turn :10-21 strand :21-40 ball-and-stick :8-10,12,15@CA,CB,CG transparency 0.6 atomcolour @* 0.1 0.1 0.8 cpk :30-35@C*,N*,O*,H*