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

Brick, Peter p.brick at imperial.ac.uk
Thu Jan 26 06:40:23 PST 2012


I've installed Phenix 1.7.3-928 on a linux workstation by downloading the binary phenix-installer-1.7.3-928-intel-linux-2.6-x86_64-fc3.tar
I'm running Red Hat Enterprise Linux Workstation release 6.2. (Mainly 64 bit libraries but some additional 32 bit libraries that are necessary to run Alwyn Jones' 32 bit version of O.)

*Help and Firefox*

When I click on the Help icon in the Phenix GUI I get the message:

[pbrick at pb1 ~/test]$ phenix
  Using browser /usr/bin/firefox
  Using browser /usr/bin/firefox
/usr/lib64/firefox-3.6/firefox: symbol lookup error: /usr/lib64/libgnome-2.so.0: undefined symbol: g_dgettext

But if firefox is already running it opens a new tab and I receive no error message. Firefox is the version shipped with RHEL 6.2: firefox 3.6.24 (I notice that the mozilla website is offering version 9.0.1 for i686 processors.)

*Starting Coot*

When I click on the Coot icon in the Phenix gui no window opens but I can see the processes: coot, coot_build_phenix_coot.csh and coot-real running. In fact coot-real consumes 100% of the cpu of one of the cores. What I find really weird is if I look at the processes with the system monitor gui and right click and 'kill' coot-real then instead of killing the process the coot window opens. At the same time coot_build_phenix_coot.csh disappears and the cpu usage drops to zero.

(Note: I've also tried the fc12 version. I found that the version of pymol distributed with phenix uses 32 bit libraries and I needed to install libXmu.so.6)

Any suggestions as to what I might be doing wrong?



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