[phenixbb] Problems with opening Coot and Firefox from gui under RHEL 6.2

Brick, Peter p.brick at imperial.ac.uk
Thu Jan 26 08:13:18 PST 2012

Many thanks for the pointers

Coot problem - mea culpa:

Instead of having the directory containing the coot script in my PATH I has defined coot as an alias. I don't understand why this caused the problem.

When compiling a 64 bit version of the ccp4 suite I found that having the coot binary folder in my path caused confusion (I think with python) and had therefore swapped to using the alias.




-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Nathaniel Echols
Sent: 26 January 2012 15:34
To: PHENIX user mailing list
Subject: Re: [phenixbb] Problems with opening Coot and Firefox from gui under RHEL 6.2

On Thu, Jan 26, 2012 at 7:27 AM, Paul Emsley <paul.emsley at bioch.ox.ac.uk> wrote:
> Another option might be that it is somehow picking up an old coot - and the
> communication dependences are not in place - however, I thought the Phenix
> gui guards against this possibility.

Not really - the rules are:

1. If the path to coot is defined in Preferences, it uses that;
2. Otherwise, if "coot" is a valid command in the shell's search path, use that;
3. Finally, look for various common places where Coot might be
expected (this is usually only necessary on Mac) for a "coot"

I may have some idea what is breaking here; will check again in a few
hours (first I need coffee).  Peter: what is the terminal output when
you click the Coot icon?

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