Re: [phenixbb] coot from phenix

Thanks, Nat, changing the preferences did the trick. Andreas On 24/10/2011 3:05, Nathaniel Echols wrote:

2011/10/24 Andreas Förster:

...

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:

/csb/soft/Linux64/share/phenix-1.7.2-869/phenix-1.7.2-869/phenix/phenix/command_line/start_coot.sh: 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?

My guess is that you had defined this in the preferences at some point - that's the only method I'm aware of for setting this path, and it's the only way to override whatever PHENIX finds by default. Open Preferences in the main GUI, click on "Graphics", and look for "Full path to Coot". If phenix.find_coot_command is locating the correct binary, you can leave that field blank.

-Nat

-- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk