[phenixbb] phenix GUI freezing during refinement and file naming issues
jmb at mrc-mbu.cam.ac.uk
Tue Dec 22 03:55:10 PST 2009
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
Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
TEL: +44 (01223) 252918
More information about the phenixbb