Pavel Afonine wrote:
Example:
phenix.refine model.pdb data.mtz strategy=individual_adp adp.individual.iso="chain A and resseq 10:20"
This will refine isotropic B-factors of atoms in residues from 10 to 20 in chain A. All the other atomic model parameters will not be refined.
Let me know if you need more examples or need any help with this.
In general, you can apply any combination of refinement strategies (coordinates, B-factors, etc..) to any selected part of your model.
Is "fix_rotamers" a strategy? Can I limit it to a selection of residues? I'm working on a large structure, and if I just say main { . . . fix_rotamers = True I get the traceback quoted below. If this is a memory problem, would fixing fewer rotamers help? Macro-cycle 0: r_work=0.2265 r_free=0.2513 Traceback (most recent call last): File "/raid/bin/phenix-1.6-289/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/raid/bin/phenix-1.6-289/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/raid/bin/phenix-1.6-289/phenix/phenix/refinement/driver.py", line 1144, in run call_back_handler = call_back_handler) File "/raid/bin/phenix-1.6-289/phenix/phenix/refinement/strategies.py", line 550, in refinement_machine log = log) File "/raid/bin/phenix-1.6-289/cctbx_project/mmtbx/refinement/fit_rotamers.py", line 391, in run map_data_3,fft_map_3 = get_map_data(fmodel = fmodel, map_type = "mFo-DFc", kick=False) File "/raid/bin/phenix-1.6-289/cctbx_project/mmtbx/refinement/fit_rotamers.py", line 307, in get_map_data map_type = map_type) File "/raid/bin/phenix-1.6-289/cctbx_project/mmtbx/map_tools.py", line 329, in fft_map symmetry_flags = symmetry_flags) File "/raid/bin/phenix-1.6-289/cctbx_project/cctbx/miller.py", line 2647, in fft_map f_000=f_000) File "/raid/bin/phenix-1.6-289/cctbx_project/cctbx/miller.py", line 3016, in __init__ conjugate_flag=True) MemoryError (later) oswego 108% cat /proc/meminfo MemTotal: 2040272 kB MemFree: 163148 kB Buffers: 156712 kB Cached: 620380 kB SwapCached: 28 kB Active: 1353300 kB Inactive: 346496 kB HighTotal: 1144828 kB HighFree: 6040 kB LowTotal: 895444 kB LowFree: 157108 kB SwapTotal: 4096564 kB SwapFree: 4096480 kB Dirty: 116 kB Writeback: 0 kB A