[Debichem-devel] Bug#472752: nable to perform "align" command (BLOSUM62 matrix not found): probably wrong path address

[Stefano Forli]

Package: pymol
Version: 0.98+0.99rc6-2
Severity: normal

Because of a wrong path definition in the
/usr/share/python-support/pymol/pymol/fitting.py:64 file, is not
possible to perform any alignment using the BLOSUM62 matrix.
The error reported by Pymol is :


Match-Error: unable to open matrix file
'/var/lib/python-support/python2.4/pymol//data/pymol/matrices/BLOSUM62'.

The line that's suppose to be related to the problem is changed in the
Sid version of the package. Is that's bug already being corrected by
updated version 1.1beta?

Wrong Line (Etch)    : [line  64]  mfile =
cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
Correct Line   (Sid) : [line 138]  mfile =
cmd.exp_path("$PYMOL_DATA/matrices/"+matrix)

-- System Information:
Debian Release: 4.0
  APT prefers stable
  APT policy: (500, 'stable')
Architecture: i386 (i686)
Shell:  /bin/sh linked to /bin/bash
Kernel: Linux 2.6.18-6-686
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)

Versions of packages pymol depends on:
ii  freeglut3              2.4.0-5           OpenGL Utility Toolkit
ii  libc6                  2.3.6.ds1-13etch5 GNU C Library: Shared libraries
ii  libfreetype6           2.2.1-5+etch2     FreeType 2 font engine, shared lib
ii  libgl1-mesa-glx [libgl 6.5.1-0.6         A free implementation of the OpenG
ii  libglu1-mesa [libglu1] 6.5.1-0.6         The OpenGL utility library (GLU)
ii  libpng12-0             1.2.15~beta5-1    PNG library - runtime
ii  python                 2.4.4-2           An interactive high-level object-o
ii  python-pmw             1.2-5             Pmw -- Python MegaWidgets
ii  python-support         0.5.6             automated rebuilding support for p
ii  python-tk              2.4.4-1           Tkinter - Writing Tk applications
ii  zlib1g                 1:1.2.3-13        compression library - runtime

Versions of packages pymol recommends:
ii  apbs                          0.4.0-2    Adaptive Poisson Boltzmann Solver

-- no debconf information