After some tries, I found that that the .reg file should be changed a little.
Then .pdb files gets icon and gets opened by pymol.cmd



"Content Type"="chemical/x-pdb"


@="PDB File"




@="\"C:\\Python27\\PyMOL\\PyMOL.cmd\" %*"


@="PDB File"




@="\"C:\\Python27\\PyMOL\\PyMOL.cmd\" %*"

2011/8/24 Troels Emtekær Linnet <>

I was very happy to find a post how to easy install pymol 1.4 from source on windows.

1) Install python, 2.5, or 2.6 or 2.7 for windows.
2) Download appropriate installer from:   Select according to your python version.
3) Run it
4) PyMOL is now installed in: C:\Python2X\PyMOL

A) C:\Python2X\PyMOL\PDB_file.reg   should be edited in a text editor, to match your python version. Run it.
B) Pymol is started by clicking C:\Python27\PyMOL\pymol.cmd   which executes python on C:\Python27\PyMOL\

Happy pymoling.