Ubuntu
pymol package

pymol can not find the BLOSUM62 matrix; wrong path

Bug #71045 reported by Adam Sjøgren
24
This bug affects 3 people
Affects Status Importance Assigned to Milestone
pymol (Debian)
Fix Released
Unknown
pymol (Ubuntu)
Fix Released
Medium
William Grant

Bug Description

When trying to align a molecule to another, Pymol reports this error:

 Match-Error: unable to open matrix file '/usr/lib/python2.4/site-packages/pymol//data/pymol/matrices/BLOSUM62'.

But pymol-package installs the file in /usr/share/pymol/matrices/BLOSUM62

(A temporary workaround is simply adding a symlink).

This is Debian bug #385550

Bug Watch Updater (bug-watch-updater)
Changed in pymol:
status: Unknown → Unconfirmed
William Grant (wgrant)
Changed in pymol:
importance: Undecided → Medium
status: Unconfirmed → Confirmed
Revision history for this message
William Grant (wgrant) wrote :

I've uploaded a fix to this.

Changed in pymol:
assignee: nobody → fujitsu
status: Confirmed → Fix Committed
William Grant (wgrant)
Changed in pymol:
status: Fix Committed → Fix Released
Bug Watch Updater (bug-watch-updater)
Changed in pymol:
status: New → Fix Released
Revision history for this message
Kayvee (vkkodali) wrote :

I am using Pymol on Jaunty and came across a similar bug.
The error I see is this:
Match-Error: unable to open matrix file '/usr/share/pymol/pymol/matrices/BLOSUM62'.

When I checked, I noticed that /usr/share/pymol directory does not have another 'pymol' directory. However, /usr/share/pymol has a 'matrices' directory in which BLOSUM62 is present. So, I created a 'pymol' directory in /usr/share/pymol and made a symlink to matrices folder there.
That fixed it! But this is something that may need to be fixed so that it works out of the box.

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