[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
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
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