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Miscellaneous Commands

The 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 typing the NOFIT command (instead of the FIT command) will set up ProFit to perform RMSd calculations but will not fit the structures. The 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 command. 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 $ is passed to the operating system exactly as given and is useful for obtaining directory listings, typing, editing or copying files.


next up previous
Next: Command Summary Up: ProFit Version 3.1 Previous: Script Files
Andrew Martin 2010-09-28