Wrong path to substitution matrix file in pymol

[Marcin Feder]

Binary package hint: pymol

It is similar to the bug nr 71045 but in Feisty the default paths have been changed. Unfortunately they are still invalid. When one tries to align any 2 structures pymol raises an exception:

PyMOL>align obj02, 2.50-A-1N1M
 Match-Error: unable to open matrix file '/var/lib/python-support/python2.5/pymol//data/pymol/matrices/BLOSUM62'.
 Error: you must first pick an atom to replace.

The simplest workaround for this problem is to create symbolink link to proper location :

sudo ln -s /usr/share/pymol /var/lib/python-support/python2.5/pymol/data/

This way we do not need modify pymol source code.

[benjou (benoit-kornmann)]

Same problem with the mutagenesis wizard.

The workaround presented here did not work.

I had to change lines 38-39 of /usr/share/python-support/pymol/pymol/wizard/mutagenesis.py

from
        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
to
        self.ind_library = io.pkl.fromFile("/usr/share/chempy/sidechains/sc_bb_ind.pkl")

as well as lines 110-111 of same file from
                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
to
                self.dep_library = io.pkl.fromFile("/usr/share/chempy/sidechains/sc_bb_ind.pkl")

And the mutagenesis works. This bug is probably present in some other scripts that I havent tested yet