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

Pavel Afonine pafonine at lbl.gov
Sat Aug 28 15:05:29 PDT 2010


  Hi Ed,

sorry for the trouble. The error you get is a memory problem indeed.

"fix_rotamers" is not a strategy. If you do:

phenix.refine --show-defaults=all

it will print out all phenix.refine parameters and you will see the list 
of "strategy" keywords:

strategy = *individual_sites individual_sites_real_space rigid_body \
                *individual_adp group_adp tls *occupancies group_anomalous

where "*" means selected.

"fix_rotamers" option may consume a lot of memory since it is using 3 
maps: mFo-DFc, 2mFo-DFc and Fc maps. All these maps are computed on the 
grid with the step high_resolution/4. I found that the scale 1./3 
sometimes works worse than 1./4, although of course using 1./3 will 
result in smaller maps.

Currently you can't select residues to apply "fix_rotamers". 
phenix.refine automatically decides which residues need a fix. The 
details of "fix_rotamers" protocol you can find here:

http://cci.lbl.gov/~afonine/rsr.pdf

My plan is :

- find a way of using less memory since it seems to be an issue for 
small memory machines/large structures;
- enable user-defined atom selection so one can apply "fix_rotamers" to 
selected residues only;
- improve quality assessment criteria to reduce false fixes.

I was working on this option beginning of this year and then I got some 
sidetracks so I still consider it "under development". For example, it 
doesn't play very well if you use NCS restraints. At low resolution I 
need to experiment with B-factor sharpened maps or/and 3Fo-2Fc or higher 
order, etc. More efficiently use H atoms.

Anyway, if you try "fix_rotamers" option I would be interested to hear 
you feedback. Thanks!

All the best!
Pavel.


On 8/28/10 9:54 AM, Edward A. Berry wrote:
> 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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