[phenixbb] coot from phenix

Andreas Förster docandreas at gmail.com
Mon Oct 24 06:48:19 PDT 2011

Dear all,

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 
started returns
/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

More information about the phenixbb mailing list