[phenixbb] coot from phenix

Nathaniel Echols nechols at lbl.gov
Mon Oct 24 07:05:37 PDT 2011

2011/10/24 Andreas Förster <docandreas at gmail.com>:
> 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.


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