Before going into the details of each of the commands, some prerequisites are necessary to describe the command flow and the standard argument types. Effectively, all the commands are processed from the input file in the order listed, except for the input/output commands. Input is the first step and involves reading in all the coordinates sets from each file specified, in the order specified, a single coordinate set at a time. For each coordinate set read in, all of the actions specified are applied and then the potentially modified coordinates are output. Not all of the actions actually modify the coordinates and some of the commands simply change the state (such as solvent which just changes the definition of what the solvent molecules are). Some of the actions just accumulate data (such as distances, angles and sugar puckers). Writing out of any accumulated data is deferred until all of the coordinate sets have been read in. Some of the actions load up contiguous sets of coordinates into main memory; with large coordinate sets this may require large amounts of memory. In these cases, such as with the command 2dRMS, it may be useful only to "save" the necessary coordinates by performing a strip of unnecessary coordinates prior to the 2dRMS call.
In the discussion that follows commands are listed in bold type.
Words in italics are values that need to be specified by the
user, and words in standard text are keywords to specify an option
(which may or may not be followed by a value). In the specification
of the commands, arguments in square brackets ([]'s) are
optional and the "|" character represents "or". Arguments that
are not in square brackets are required. In general, if there is an
error in processing a particular action, that action will be ignored
and the user warned (rather than terminating the program), so check
the printed WARNING's carefully... In what follows is listed a few
standard argument types:
mask: this is an atom or residue mask; it represents the list of
active atoms. The current parser recognizes a simplified midas style format
for picking atoms and residues. The "@" character represents an
atom selection and the ":" character represents a residue
selection. Either the atom and residue names or numbers can be specified. The
"-" character represents a continuation. The "~" represents
"not" and in this naive implementation, if this character is specified
anywhere in the string, the "not" flag will be turned on.
The "*" character is a wild card and will match all the atoms if specified alone.
When specified in atom or residue name specifications, sometimes it will
correctly work as a wildcard. The "?" character is also a wildcard, however only
one character is matched. Note that the current parser is really very stupid. Hopefully this
will be fixed to properly handle
quoted strings and spaces. Until this is "fixed", check the output
very carefully; note that whenever an atom mask is used, a summary of
the atoms selected is printed, so check this out...
filename: this refers to the full path to a file and note that no checking is done for existing files, i.e. data will be overwritten if you attempt to write to an existing file.