[phenixbb] Bad selections in phenix.refine

Nathaniel Echols nechols at lbl.gov
Sun Jul 11 18:18:31 PDT 2010

On Sun, Jul 11, 2010 at 5:36 PM, Mark A Saper <saper at umich.edu> wrote:

> When running phenix.refine from the GUI, definitions for rigid body groups
> in phenix.refine that are syntactically wrong, causes the job to just hang
> with "running" status but no CPU is used.  It would be nice if either the
> GUI checked for valid selections, or if phenix.refine returned an
> appropriate error code that would be recognized by the GUI.

Actually, the latter is exactly what should happen - the only reason why it
wouldn't is if you've stumbled across a low-level C++ error that can't be
propagated.  I already modified the code to handle one such error a couple
of months ago (it should be in 1.6.2) but there may be others I don't know
about.  The best way to check this is to run phenix.refine on the command
line using the .eff file written by the GUI, which should end with a
recognizable error message.  (You can just send me the input files if you
want.)  However, I will try reproducing it myself with a test structure

You can validate the selections in the GUI by clicking the "view/pick"
button next to the input widget, which will load up the simple graphics
window with your start model.  It should be very obvious if the selection
string is syntactically incorrect.  Validating these automatically at
runtime would be nice but it's more difficult (and time-consuming).

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