On Sat, Aug 28, 2010 at 9:54 AM, Edward A. Berry
Is "fix_rotamers" a strategy? Can I limit it to a selection of residues?
I think it's only global right now.
I get the traceback quoted below. If this is a memory problem, would fixing fewer rotamers help? File "/raid/bin/phenix-1.6-289/cctbx_project/cctbx/miller.py", line 3016, in __init__ conjugate_flag=True) MemoryError
Sorry, it is crashing during an FFT, which is required to generate the maps used for fitting, and I believe this has to be done over the entire unit cell. I suspect there are some inefficiencies in the code, because I've seen this same error before in GUI bug reports. (For instance, the grid spacing is 1/4 of resolution, and changing to 1/3 might fix the problem - although it will probably also have a negative effect on the real-space refinement.) Regardless, the only solution is to upgrade the RAM, and since you already have 2GB installed, you will also need to upgrade to a 64-bit OS and Phenix installer if you aren't already using that. (This assumes that your processor is compatible, of course.) PS. Please update to version 1.6.4, I believe Pavel made some major improvements to the rotamer fitting since 1.6 was released (and of course there are many other new features/fixes as well). -Nat