[phenixbb] coot from phenix

Andreas Förster docandreas at gmail.com
Mon Oct 24 07:23:08 PDT 2011

Thanks, Nat, changing the preferences did the trick.


On 24/10/2011 3:05, Nathaniel Echols wrote:
> 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.
> -Nat


         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London

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