Monday, October 17, 2011

PDB V3 to V2 file converter and CamShift 1.35 notes


I stubmled upon a program called CamShift 1.35, which predicts chemical shifts from a coordinates in a PDB file. However, everytime I tried to supply it with a seemingly  standard PDB file, adhereing to every PDB naming convention I could find, CamShift 1.35 would complain about missing atoms and used an internal force-field to add hydrogens and whatnot at coordinates that were not correspoding to the coordinates I had supplied.
A little trick I found, was to uncomment the lines 278-279 in the camshift-1.35/bin/camshift.cpp file:

//  for(int r=0;r<rep.size();r++)
//    cout<<"\t"<<p.atom_name(rep[r],Almost::Protein::BASE)<<"\n";

 and the recompile. This will add the names of all atoms that are added. Please note, that protonation states are adjusted entirely by CamShift, so even if you give it a proper PDB file you will have things added, such as H-gamma on cysteine residues, even despite of actual cys-bridges in the supplied PDB file.

At any rate, by doing the above, I discovered that the CamShift 1.35 code uses the old PDB v2 naming convention (which was deprecated during the last millennium). Sadly I couldn't find any file converter that would let convert a standard (currently PDB v3) PDB file to an older v2 type. Not even my all-time favourite file-converter OpenBabel was capable of this. Long story short, I found the proper naming conversions and put it in a short python script.

Usage is like this:

$ python pdb_v3_to_v2.py myfile.pdb

This will print the new file to standard out put. If you want it in a new file, simply use the awesomeness of shell:

$ python pdb_v3_to_v2.py myfile.pdb > outfile.pdb

Since it's written in standard Python, it will work on any platform (Windows, UNIX, Linux, MacOS, etc) and you need not worry about compiling, just a working Python interpreter is enough.


Have fun converting. Shoot me a message, if you find any bugs or quirks. Download the program here:


(click link or picture to download)

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