[phenixbb] phenix GUI freezing during refinement and file naming issues

John Berrisford jmb at mrc-mbu.cam.ac.uk
Tue Dec 22 03:55:10 PST 2009

Dear all

I've recently been having a few problems with the new phenix GUI 
freezing during refinement runs on several different systems, most often 
when I try and do something different on the computer which puts the GUI 
in the background or on a different desktop.

I've seen this problem when running a local copy of phenix on a ubuntu 
9.10 system or when running the GUI remotely on a mac connected to our 
Centos linux cluster. When I switch to a different desktop to get on 
with doing something else (refine jobs can take a long time) the GUI 
freezes - although the underlying task runs correctly. The only way out 
of this problem is to force quit the GUI and then restart it. However, 
this means that the task isn't recorded in my history and all settings 
used to run the job are lost from the GUI - the parameter file to run 
the job does exist though. This also means I lose all the nice 
molprobibity connections to coot which are really useful. Also if I try 
to run phenix on the Centos linux cluster when running a local windows 
system the GUI is so sllloooowwww whenever the GUI tries to open a new 
window that its unsuable.
Has anyone else seen these problems and know a cure?
If I run phenix locally on a mac I don't seem to have this problem, but 
it is nice to run the refine job on our linux cluster so that I can get 
on with doing something else without it slowing down my mac.

On another note, when running phenix refine from the GUI it nicely puts 
all the files in a folder called "Refine_1" etc... with the number 
incrementing with each run. So, why are the pdb and mtz file always 
called "refine_1..." not "refine_2 etc... to match the folder name? This 
would help with keeping track of files during itterative refinement and 
model building. It would also stop the problem of having lots of files 
called "refine_1" loaded into coot when I try to compare models from 
different refine runs.
It would also be useful to be able to be able to add a prefix to the 
file name / folder name / job name in the GUI so that I could 
distinguish between different refinement experiments. This is easy to do 
on the command line....

Thanks and merry christmas


John Berrisford

Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road
WEB: www.mrc-mbu.cam.ac.uk
TEL: +44 (01223) 252918

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