[phenixbb] phenix.refine frozen

Nathaniel Echols NEchols at lbl.gov
Thu Feb 11 10:14:28 PST 2010

On Feb 10, 2010, at 11:13 PM, Roberto Steiner wrote:
> I am playing around with phenix.refine which comes with Phenix distro 1.6-289 for Mac-Intel. When running a normal refinement job
> (ind site + grouped ADPs + ncs+TorsionSimulatedAnnealing) phenix.refine gets stuck after bulk solvent modelling and scaling.

This sounds like a problem with phenix.refine, not the GUI.  One possible issue that I discovered yesterday is that there are certain errors that can't be propagated to the GUI - the job crashes, but the GUI still thinks that it's running.  These are typically very low-level errors; this is basically impossible to debug without having the data (and it may be system-dependent as well; what platform are you running it on?).  The only thing I can suggest in this case is to try running the same refinement on the command line - it may at least print an interpretable error message.

> Additionally, if I click on the abort button on the bottom-left of the page nothing happens. On the other hand
> if I click on the abort icon at the top of the page I get the message
> "You are not currently running any calculations. Do you want to close this window?"
> If I say Ok the following message appears:
> "There is at least one process running; are you sure you want to exit before it is finished"

Part of this is probably a bug.  Because of the way processes are handled in 1.6, the abort request won't be carried out if the process is simple non-responsive.   What does it say on the status bar (the strip at the bottom of the window), and is the little color-cycle widget at the bottom of the right still animated?  If the process is still running, it will say so.

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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