On Mon, Jul 22, 2013 at 2:13 PM, Joseph Noel
Has anyone had a problem when using Phenix refine through the GUI on a Mac wherein the program after hitting Run locally starts but then hangs without proceeding? Seems to happen to me about one out of five times I run refine and always hangs when I experiment with ramachandran restraints for only a portion of the polypeptide chain. I've tried letting things alone for several hours and nothing happens. I can abort and then often resubmit and it then runs fine (except for rama restraints). I've found this happens with both nightly builds and stable releases. I am currently running the latest nightly build 1439.
I guess the moral here is "never use Ramachandran restraints", which is good advice under nearly any circumstances, but this sounds like a bug we need to address. A few follow-up questions: 1) Can you please send me all inputs off-list? The .eff file would be helpful too - you can get to this from the job history tab by clicking "Show details". 2) Open the console (in /Applications/Utilities) and look for suspicious error messages. In particular, I get occasional mysterious crashes which output a mention of "malloc", and the phrase "set breakpoint to debug". (Totally unrelated to Ramachandran restraints, as far as I know.) thanks, Nat