[phenixbb] coot from phenix
docandreas at gmail.com
Mon Oct 24 06:48:19 PDT 2011
I'm running phenix 1.7.2-869 on RHEL 6.1 64-bit. When I click on "Open
in Coot" after refinement, coot doesn't open and I get the following
error in the shell from which I started phenix:
line 33: /csb/soft/Linux/src/coot-0.6/bin/coot: No such file or directory
In the script that launches coot, $PHENIX_COOT is defined as
/csb/soft/Linux/src/coot-0.6/bin/coot, which doesn't exist (and is a
path that we used in the old days of 32-bit).
Typing phenix.find_coot_command in the shell from which phenix was
/csb/soft/Linux64/src/coot-0.7-rev3689/bin/coot, which is the right coot.
To me it seems the phenix script to launch coot is falling back on an
internally defined $PHENIX_COOT variable (that's not defined from the
shell). That's shouldn't be, should it? How do I fix this short of
hardwiring $PHENIX_COOT as /csb/soft/Linux64/src/coot-0.7-rev3689/bin/coot?
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
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