[phenixbb] Can Phenix fix rotamers for several residues only?

Edward A. Berry BerryE at upstate.edu
Sat Aug 28 09:54:26 PDT 2010

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
   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 
     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
   File "/raid/bin/phenix-1.6-289/cctbx_project/cctbx/miller.py", line 3016, in __init__

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

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