RMS command may be used to reprint the RMS deviation over
the currently defined set of RMS zones and RMS atoms.
If you simply wish to calculate the RMSd between two or more structures
without actually fitting them, defining fitting regions in the normal way then
NOFIT command (instead of the
will set up ProFit to perform RMSd calculations but will not fit the structures.
RMS command can then be used to print the RMS deviation.
As of ProFit V3.0 it is possible to match symmetrical atoms automatically in
amino acid sidechains (e.g.CD1 - CD2 and CE1 - CE2 of tyrosine) using the
SYMMATOMS matches the charged oxygens and
nitrogens on arginine, aspartate and glutamate residues and the delta and
epsilon carbons of phenylalanine and tyrosine residues. It is also possible
to match the nitrogen and oxygen atoms of the amide
sidechains of asparagine and glutamine residues and the prochiral methyl
groups of valine and leucine. Typing
SYMMATOMS will display the pairs
of atoms currently matched by ProFit. Typing
SYMMATOMS ON or
SYMMATOMS OFF will turn symmetrical atom matching on or off.
Individual residue types, for example ASP, can be turned-on or off by
typing SYMMATOMS ASP ON or SYMMATOMS ASP OFF, respectively. Alternatively,
SYMMATOMS ALL ON will turn all atom pairs on. By default, the matching of
symmetrical atoms is turned-off.
Any operating system command may be run from within ProFit by
preceding it with a
$. The string following the
passed to the operating system exactly as given and is useful for
obtaining directory listings, typing, editing or copying files.