ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate program for performing least squares fits of two or more protein structures. It performs a very simple and basic function, but allows as much flexibility as possible in performing this procedure. Thus one can specify subsets of atoms to be considered, specify zones to be fitted by number, sequence, or by sequence alignment.
The program will output an RMS deviation and optionally the fitted coordinates. RMS deviations over alternate zones and atoms may also be calculated without performing a new fit. Thus the zones for calculating the RMS deviation can be different from those used for fitting.
While optimised for proteins, non-protein structures may also be fitted if they are stored in the standard Protein Databank (PDB) format.
ProFit is written to be as easily portable between systems as possible and uses a command-driven interface.
ProFit uses the McLachlan fitting algorithm, essentially a steepest descents minimisation, as described in McLachlan, A.D. (1982) Rapid Comparison of Protein Structures, Acta Cryst. A38, 871-873. This part of the code is based on an implementation by Dr. Mike Sutcliffe.
Type module avail ProFit at the prompt
How to Use
Coot uses environment modules. Typemodule load ProFit
then type profit at the prompt, input is menu-driven:[helix]$ profit
For non-interactive (commandline) use, the syntax is:Syntax: profit [-h] [-f <scriptfile.txt>] [<reference.pdb> <mobile.pdb>] -h Include HETATM records when reading PDB files -f Run script