ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate least squares fitting program.

It has many features including:

  • flexible specification of fitting zones and atoms (including by sequence),
  • automated generation of fitting zones by sequence or structural alignment,
  • calculation of RMS over different zones or atoms,
  • RMS-by-residue calculation, on-line help facility,
  • Multiple structure fitting
  • ...

The program will output an RMS deviation and optionally the fitted coordinates. RMS deviations may also be calculated without actually performing a fit. Zones for calculating the RMS can be different from those used for fitting.

Online Server

The online server provides access to basic simple functionality of ProFit.

ProFit Server


ProFit is a command-driven program for which you need to learn its command syntax. Full documentation is provided as a PDF file.


FAQs and notes

There is a detailed FAQ (frequently asked questions) with information about using ProFit.

Important warning about using HETATMs and changes in ProFitV2.2!

ProFit FAQ


ProFit is freely available for use by not-for-profit organisations and for commercial organisations (providing they inform the author that they are using it). It may not be distributed without the author's permission, but must be obtained from this site. It is supplied as a gzipped tar file of source code and as an Linux binary.

Information on how to install our software.

As of V3.1, a Windows version is fully supported. We thank Bernhard Rupp who previously provided a Windows version of ProFitV2.3.

Download ProFit ProFit README Run via Docker


Development of V2.6-V3.1 performed by Dr. Craig T. Porter has been funded by the BBSRC.

BBSRC logo

NEW! ProFit V3.3 (released 28.04.2020)

V3.3 Adds support for reading individual models from a PDB file. This is done by adding %n to a filename (where n is the model number). For example, pdb2kqn.ent%2 will read MODEL 2.

Note that ProFit V3.2 was never publicly released.

ProFit V3.1 (released 03.04.2009)

V3.1 Adds Windows support. You can now download a Windows executable or compile the source for Windows yourself.

V3.1 also fixes a small bug in NOFIT support and with a problem in specifying 3-letter atom names in the ATOMS and RATOMS commands.

ProFit V3.0 (released 27.02.09)

V3.0 addresses a number of new features and fixes mostly related to multiple structure and multiple chains as well as a number of minor fixes and new features requested by users:

  • Multiple structure fitting now gives RMSD to first mobile structure by default.(SETREF)
  • Calculation of the averaged reference structure for multiple structure fitting is now weighted by the number of mobile structures.(WTAVERAGE)
  • Can fit multiple structures in order of RMSD.(ORDERFIT)
  • Can run an all vs all comparison of mobile structures. (ALLVSALL)
  • Can match symmetrical atoms.(SYMMATM)
  • Can perform iterative fitting on structures with more than one chain.
  • Can read PIR alignments with more than one chain.(READALIGN)
  • Can align structures with more than one chain.(ALIGN)
  • Can output fitting zones as an alignment.(PRINTALIGN)
  • Added support for GNU Readline library.

What people are saying about ProFit

  • Just downloaded ProFit on the recommendation of a collegue and got the answer I wanted within 5 minutes, what a fantastic program, easy to 'install' and elegant and simple syntax (can you tell I'm not used to this!!!).

    A user from Cambridge

  • Following the instructions in the on-line documentation, I was able to quickly compute the rmsd between structures in two pdb files.... Thank you for offering this program for use by the research community.

    A user from Los Alamos

  • Thanks a lot for writing such an useful piece of software and more importantly for documenting it and providing it for our use.

    A user from the University of Chicago

  • I am using Profit to calculate the interface RMSD between a reference protein heterodimer and different conformations of this dimer generated by docking. I must tell you how useful this tool has been in my project. I am very grateful to you for having created this tool and for having made it free of charge.

    A user from India