Bug 215602 – pymol: wrong path to matrices

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Bjoern Olausson 2008-03-31 16:42:46 UTC]

When you try to align two molecules, you get the following error:

Match-Error: unable to open matrix file '/usr/lib/python2.5/site-packages/pymol/data/pymol/matrices/BLOSUM62'.

Actually the file is located in
/usr/share/pymol/data/pymol/matrices/BLOSUM62

For a fast fix, just symlink it.

Same bug was filed here:
https://bugs.launchpad.net/ubuntu/+source/pymol/+bug/71045

Reproducible: Always

Steps to Reproduce:
1.Align two molecules with pymol
2.
3.




sci-chemistry/pymol-1.0-r1

[Comment 1 Bjoern Olausson 2008-03-31 16:44:52 UTC]

ln -s /usr/share/pymol/data /usr/lib/python2.5/site-packages/pymol/data

[Comment 2 Justin Lecher (RETIRED) 2008-03-31 17:51:14 UTC]

Should reported upstream. I think pymol doesn't query in $PYMOL_DATA/pymol/matrices/BLOSUM62.

[Comment 3 Donnie Berkholz (RETIRED) 2008-03-31 20:00:43 UTC]

It's not upstream, it's because we try to move files to FHS locations. Pymol has environment variables to allow for this, but some files still need patching. Looks like one more place to patch.

[Comment 4 Justin Lecher (RETIRED) 2008-03-31 20:34:47 UTC]

No it isn't.

Upstream says:
"The bug was arising from PyMOL's incorrect use of PYMOL_PATH/data in fitting.py, which has now been replaced with $PYMOL_DATA in the SVN source."

I tried to reproduce the bug with latest svn source and couldn't. The latest portage version is still Broken. 

Here is the patch:

--- fitting.py.orig     2008-03-31 22:33:29.000000000 +0200
+++ fitting.py  2008-03-31 22:33:46.000000000 +0200
@@ -135,7 +135,7 @@
         if string.lower(matrix)=='none':
             matrix=''
         if len(matrix):
-            mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
+            mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
         else:
             mfile = ''
         if object==None: object=''

I will update the ebuild tomorrow. 

[Comment 5 Donnie Berkholz (RETIRED) 2008-03-31 20:44:46 UTC]

OK, thanks for pursuing that. It's worth knowing the above information anyway.

[Comment 6 Bjoern Olausson 2008-03-31 20:48:17 UTC]

Thanks for the fast response... 

justin was faster than me.

--> With the latest SVN version it works

I just released an ebuild for http://mgltools.scripps.edu/
just in case anyone is interested in maintaining it or to pull it into portage
It's the GUI to sci-chemistry/autodock

kind regards
Bjoern

[Comment 7 Justin Lecher (RETIRED) 2008-04-01 12:00:24 UTC]

I figured our what the problem is:
PYMOL_DATA is set to /usr/share/pymol/data. The pymol-data-path.patch corrects the paths to PYMOL_DATA/data but it should be just PYMOL_DATA. I add the updated patch. Other wise the PYMOL_DATA could set to /usr/share/pymol/, which i think is not the better solution.

The revision from yesterday only needs commanding.py and importing.py tpo be patch, so pymol-9999-data-path.patches must be updated.

[Comment 8 Justin Lecher (RETIRED) 2008-04-01 12:02:06 UTC]

Created attachment 147966 [details]
pymol-1.0-r1-data-path.patch.new

[Comment 9 Donnie Berkholz (RETIRED) 2008-07-07 05:15:52 UTC]

Justin, is this fixed in the ebuild in the science overlay?

[Comment 10 Donnie Berkholz (RETIRED) 2008-07-07 05:21:52 UTC]

Please reopen if it's not fixed.

[Comment 11 Justin Lecher (RETIRED) 2008-07-07 07:27:42 UTC]

It is fixed.