On Mon, Mar 28, 2011 at 5:59 AM, Kendall Nettles
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 too. 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. -Nat