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

Paul Emsley paul.emsley at bioch.ox.ac.uk
Thu Jan 26 07:27:41 PST 2012

> *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?

That sounds like a startup-script problem (race condition?).  When you 
send coot the TERM signal, it stops waiting for communication and gets 
on with starting up - presumably as it would if you started it without 
Phenix (if one can contemplate such a thing).

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.


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