Phenix "hangs" on a Mac?
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. ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected] Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________
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
On 7/22/13 2:22 PM, Nathaniel Echols wrote:
I guess the moral here is "never use Ramachandran restraints",
hard to agree, page 49-55: http://www.phenix-online.org/presentations/latest/pavel_refinement_general.p... If you know what you do and use them right it may be a good thing to do. After all, you can crack your finger with a hammer, which obviously doesn't mean you should never use it. Pavel
participants (3)
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Joseph Noel -
Nathaniel Echols -
Pavel Afonine