[phenixbb] differences between command line and GUI?

Nathaniel Echols nechols at lbl.gov
Mon Mar 28 07:31:53 PDT 2011

On Mon, Mar 28, 2011 at 5:59 AM, Kendall Nettles <knettles at scripps.edu> wrote:
> I ran a job through the GUI, and then what I thought was the same job on our cluster. The job from the cluster has Rfree that is 0.7% higher. I'm totally at a loss to figure out what is causing this. It is the same version of PHENIX (1.7-650). I then took the .eff file from the GUI job and used that as the params file for the command line job but still get the big difference in R free. Any suggestions?

Which program?  Try running 'diff' on the .eff files for jobs that
produced different R-frees and see what the exact differences are.

If you were running phenix.refine, there are two points where the
parameters diverge in 1.7:

1) The command-line version reads in an additional set of parameters
for real-space refinement, modifying the defaults (since these are
used elsewhere for very different purposes, we need two sets of
defaults).  The GUI doesn't do this, because I wasn't aware of it at
the time.  Next version will use the same parameters for both (as soon
as I fix it...).

2) The GUI sets the maximum RMS(bonds) and RMS(angles) for weight
optimization much lower than the defaults for the command-line
version, which I felt were unreasonably high (and led to geometry
problems for some structures).  It appears that the defaults are now
closer to what I set, so it may be time to remove this discrepancy

Either of these could explain the difference in R-free.  However, as
Tom points out, many programs will come up with a slightly different
answer depending on where they are run, often for reasons that don't
make sense.  If you switch between Mac and Linux, you'll almost
certainly see this happen regularly.


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