judyphan26 / calibur

Source codes for the Calibur program reported in https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-25

This is the source codes for the Calibur program reported in https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-25

(For precompiled Windows binary of Calibur, please visit https://sourceforge.net/projects/calibur/)

How to compile:

If you are running a variant of UNIX (or MacOS/WSL/Cygwin/MSYS2), you should have the GNU C compiler (gcc) and Make (make) installed. At the directory where the file Makefile is, type make. This will build two programs: calibur and calibur-lite

• calibur is the main program.
• calibur-lite is a lighter version of calibur which reports only the best decoy.

If you are running MS Windows, you should have installed MS Visual Studio Community. Open the Developer Command Prompt at the directory where the file Makefile.win is, type nmake /F Makefile.win. This will build the program calibur.exe.

That's all!

How to run:

1. Prepare a file which list all the decoys' PDB files. That is, the file should read like:

decoysdir/1enhA0.pdb
decoysdir/1enhA1000.pdb
decoysdir/1enhA1001.pdb
decoysdir/1enhA1002.pdb
decoysdir/1enhA1003.pdb
...

Alternatively, you can use Rosetta's compose_score_silent.py to create a silent file out of your PDB files, and use this file as input to calibur.

2. Call calibur with this filename (mydecoys say) as the only parameter

   sh> calibur mydecoys (or sh> ./calibur mydecoys, or C:\> .\calibur mydecoys according to your system setup)

   calibur will figure out a reasonable threshold itself. You can also specify a threshold. For example, for threshold 1.0, run calibur as

   sh> calibur mydecoys 1.0

   You can also change the strategy that calibur uses to discover the threshold. To see how, run

   sh> calibur

   And the options will be shown.