ProFit: FAQs
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- How do I cite ProFit?
- I want to fit two regions of different length. How can I specify a ZONE?
- Can I run ProFit under Mac OS/X?
- How can I run ProFit from a script?
- How do I run ProFit in Windows
How do I cite ProFit?
This question is answered on the last page of the manual!
From the manual...
How do I Reference ProFit?
No paper has been published describing ProFit itself since it is simply a convenient program (I hope) to let you use a standard fitting algorithm; consequently, it is a little difficult to reference. The exact wording is up to you and dependent on the context, but I suggest something similar to:
Fitting was performed using the McLachlan algorithm (McLachlan, A.D., 1982 ``Rapid Comparison of Protein Structres'', Acta Cryst A38, 871-873) as implemented in the program ProFit (Martin, A.C.R.,
http://www.bioinf.org.uk/software/profit/).
I want to fit two regions of different length. How can I specify a ZONE?
It is not possible to compare regions of different length! The definition of an RMSD requires that there be a 1:1 equivalence between atoms. Therefore, you must somehow decide which residues are equivalent to one another. Typically you would do this with a structural alignment program such as SSAP rather than a least-squares fitting program like ProFit.
That said, ProFit has the ability to work out the best equivalences once you have given it a seed set. Typically you perform a sequence alignment between the two regions (either externally and read it in using the READALIGNMENT command, or internally by using the ALIGN command). That gives the program a starting point for equivalent pairs of atoms. You can then use the ITERATE command to get ProFit to refine the equivalences which it does using a dynamic programming algorithm.
Can I run ProFit under Mac OS/X?
Yes! I don't have a Mac OS/X machine so I can't verify this from personal experience. I'd like to thank Judith Cohn (Los Alamos National Lab), Nicola Ramsden (Dundee) and Michael Plevin (Toronto) for pointing out problems and testing that the code compiles.
How can I run ProFit from a script?
One of the most common questions I get about ProFit is something along the lines of 'I have lots of pairs of proteins I need to fit or one protein that needs to be fitted to lots of others. How can I get ProFit to process all of these?'
The answer is very simple and relies on just using Unix-style redirection. Just place all the commands you wish to run in a text file and then run ProFit, redirecting standard input to this file.
For example, suppose you wanted to use a.pdb as a reference structure and wanted to fit it with b.pdb, c.pdb, d.pdb, e.pdb and f.pdb. Just create a text file as follows:
reference a.pdb mobile b.pdb fit mobile c.pdb fit mobile d.pdb fit mobile e.pdb fit mobile f.pdb fit
If you have called this file profit.in, them you just run ProFit with the command:
profit < profit.in
Of course the input file should also include any other commands you need such as specifying the atoms for fitting or the ranges over which to fit.
How do I run ProFit in Windows?
The short answer is "don't"! I don't support a Windows version. You should be able to compile ProFit under Windows, but you are on your own if you try!
I do provide a precompiled Windows version, but it is (a) old and (b) completely unsupported.
That said, here are a couple of pointers. When you unpack the ZIP file, you will end up with two files: profit.exe and prof.cmd (The extensions may not be visible in Windows if you haven't removed the option to hide extensions.)
prof.cmd is a simple demonstration command file of how to run a ProFit command from a script. profit.exe is the actual program.
ProFit doesn't have a Windows interface - it is command line driven and you need to run it from a DOS shell. So open an MS-DOS shell, go to the directory where you unpacked ProFit and type the command:
profit
You will then be in the ProFit command interface.
From there on, you need to read the documentation. See the main ProFit web page. (Note that the online documentation is for the latest version and not the Windows version, so not all features are available.)
