[27439] in Athena Bugs
Re: Debathena: pymol
daemon@ATHENA.MIT.EDU (Alex T Prengel)
Tue Mar 30 16:25:56 2010
Message-Id: <201003302025.o2UKPp8e013898@dit.mit.edu>
To: kromer@mit.edu
In-reply-to: "[27434] in Athena Bugs"
Date: Tue, 30 Mar 2010 16:25:51 -0400
From: Alex T Prengel <alexp@mit.edu>
Cc: alexp@mit.edu, bugs@mit.edu
Errors-To: bugs-bounces@mit.edu
Hi Katherine,
>What were you trying to do?
> align two structures using pymol
>What's wrong:
> get the error message "Match-Error: unable to open matrix file
> '/usr/share/pymol/pymol/matrices/BLOSUM62"
>What should have happened:
> Should have aligned the structures with no error
>Please describe any relevant documentation references:
>Alignment matrices are actually in /usr/share/pymol/matrices/ rather
>than in /usr/share/pymol/pymol/matrices. I can fix this problem for
>myself by doing sudo mkdir /usr/share/pymol/pymol; sudo ln -s
>/usr/share/pymol/matrices/ /usr/share/pymol/pymol/matrices, but it
>would be nice if it were fixed for everyone.
Thanks for reporting these details. This appears to be a known issue
as it turns up in various places in Ubuntu's bug tracking system. We
will try to make sure it's been reported upstream, and we'll
investigate the possibility of making a local fix in the next
debathena release.
This isn't a trivial matter as our standard policy is to install
unmodified Ubuntu packages for Third Party applications like pymol,
and making local modifications is likely to be problematic for a
variety of reasons.
Alex Prengel
IS&T Faculty/Student Experience
