[phenixbb] AUTOSOL for MAD data with error message-'Need a symfile for solve'

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Feb 2 09:26:37 PST 2010


Hi Frank and Graeme and Mohan,

Yes, P 2 21 21 should be allowed in autosol. I see that it doesn't work
and I'll fix that.

All the best,
Tom T


>> Um, this one has been hacked to death on ccp4bb:  there is in fact
>> nothing wrong or "non-standard" with that setting.  If the program won't
>> handle it, email the authors and ask them to fix it.
>>
>> Reindexing is an almighty pain in the butt.
>>
>> That said:  it sounds like you may be pointing at an out-of-date
>> symmetry operator file;  I forget which environment variable it is,
>> check the manual, but point it to an up-to-date ccp4 installation, and I
>> suspect it will be fine.
>>
>> phx
>>
>>
>>
>>
>> On 02/02/2010 13:49, Graeme Winter wrote:
>>> Hi Mohan,
>>>
>>> P22121 is not the standard setting for this spacegroup - in
>>> International Tables the convention is to have the spacegroup's unique
>>> axis as C, e.g. P21212 in this case. If you run this reflection file
>>> through reindex as follows:
>>>
>>> reindex hklin in.mtz hklout out.mtz<<  eof
>>> reindex k,l,h
>>> eof
>>>
>>> Then it should work just fine. An alternative would be to compose a
>>> solve "symm" file and put this in the right place. This would look
>>> something like:
>>>
>>>    4 Equiv positions, P22121     SG #  3018
>>>   X,Y,Z
>>>   X,-Y,-Z
>>>   -X,1/2+Y,1/2-Z
>>>   -X,1/2-Y,1/2+Z
>>>
>>> (copied from spacegroup #3018 in the CCP4 symop.lib) which would need to
>>> go in
>>>
>>> phenix-1.6-289/solve_resolve/ext_ref_files
>>>
>>> On balance, reindexing is probably easiest!
>>>
>>> Best wishes,
>>>
>>> Graeme
>>>
>>> On 2 February 2010 13:38,<m.b.rajasekaran at reading.ac.uk>  wrote:
>>>
>>>>
>>>> Dear all,
>>>>              I have a query regarding the Autosol option in the
>>>> PHENIX-1.6-289 version. We are trying to process a MAD data for a zinc
>>>> bound
>>>> protein crystal with AuTOSOL. We uploaded the scaled files, sequence
>>>> and all
>>>> other details and started running AUTOSOL. But the program stopped with
>>>> the
>>>> following error message pasted below mentioning some missing of
>>>> symfile. We
>>>> were not able to locate any parameters file on the installation
>>>> directory.
>>>> It would be helpful if we get some useful suggestions on this.
>>>>
>>>> Thanks in advance,
>>>> Mohan
>>>> ***********************************************************
>>>>
>>>>          PHENIX AutoSol  Tue Feb  2 12:37:41 2010
>>>>
>>>> ************************************************************
>>>>
>>>> Working directory:  /home/sar06mbr/30JanDiamondI02/107/107_php22121
>>>> PHENIX VERSION: 1.6 of 29-01-2010 PHENIX RELEASE_TAG : 289 PHENIX MTYPE
>>>> :
>>>> intel-linux-2.6 PHENIX MVERSION : suse AutoSol_start AutoSol Run 2 Tue
>>>> Feb 2
>>>> 12:37:41 2010 INPUT FILE LIST:
>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz',
>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz',
>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz']
>>>>
>>>> Copied /home/sar06mbr/30JanDiamondI02/107/107_php22121/result.seq to
>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/AutoSol_run_2_/sequence_autosol.dat
>>>>
>>>> Setting chain_type to PROTEIN Setting defaults for data_quality
>>>> moderate
>>>> Setting thorough_denmod to Yes Settin fix_xyz_after_denmod to False
>>>> Setting
>>>> max_ha_iterations to 2 Setting fixscattfactors to No Settin defaults
>>>> for
>>>> thoroughness quick Setting best_of_n_hyss_always to 1 Setting
>>>> max_extra_unique_solutions to 0 Settin ha_iteration to No Setting
>>>> max_choices to 1 Setting number_of_models to 1 Setting number_of_builds
>>>> to 1
>>>> Setting test_mask_type to No Setting n_cycle_build to 0 Setting
>>>> thorough_loop_fit to Setting create_scoring_table to No Not truncating
>>>> ha
>>>> sites at start of resolve as this is not PHASER SAD phasing
>>>>
>>>> Trying to guess refinement file for later use from
>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz',
>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz',
>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz']
>>>>
>>>> Choosing guess of refinement file for later use from all files:
>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz',
>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz',
>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz']
>>>>
>>>> FILE TYPE ccp4_mtz
>>>>
>>>> COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re',
>>>> 'SIGF_107_2re',
>>>> 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)',
>>>> 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re',
>>>> 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)']
>>>>
>>>> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1',
>>>> 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90)
>>>> Space
>>>> group: P 2 21 21 (No. 18) CONTENTS:
>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz',
>>>> 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344,
>>>> 108.92009735107422,
>>>> 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1',
>>>> 'SIGF1',
>>>> 'DANO1', 'SIGDANO1']]
>>>>
>>>> File
>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz
>>>> RES: 2.5
>>>>
>>>> FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag',
>>>> 'F_107_3re',
>>>> 'SIGF_107_3re', 'F_107_3re(+)', 'SIGF_107_3re(+)', 'F_107_3re(-)',
>>>> 'SIGF_107_3re(-)', 'DANO_107_3re', 'SIGDANO_107_3re', 'IMEAN_107_3re',
>>>> 'SIGIMEAN_107_3re', 'I_107_3re(+)', 'SIGI_107_3re(+)', 'I_107_3re(-)',
>>>> 'SIGI_107_3re(-)']
>>>>
>>>> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1',
>>>> 'DANO1', 'SIGDANO1'] Unit cell: (34.85, 109.18, 135.27, 90, 90, 90)
>>>> Space
>>>> group: P 2 21 21 (No. 18) CONTENTS:
>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz',
>>>> 'mtz', 'premerged', 'P 2 21 21', [34.849998474121094,
>>>> 109.18000030517578,
>>>> 135.26980590820312, 90.0, 90.0, 90.0], 2.4889952912293629, ['F1',
>>>> 'SIGF1',
>>>> 'DANO1', 'SIGDANO1']]
>>>>
>>>> File
>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz
>>>> RES: 2.5
>>>>
>>>> FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag',
>>>> 'F_107_4re',
>>>> 'SIGF_107_4re', 'F_107_4re(+)', 'SIGF_107_4re(+)', 'F_107_4re(-)',
>>>> 'SIGF_107_4re(-)', 'DANO_107_4re', 'SIGDANO_107_4re', 'IMEAN_107_4re',
>>>> 'SIGIMEAN_107_4re', 'I_107_4re(+)', 'SIGI_107_4re(+)', 'I_107_4re(-)',
>>>> 'SIGI_107_4re(-)']
>>>>
>>>> GUESS FIL TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell:
>>>> (34.87, 109.2, 135.33, 90, 90, 90) Space group: P 2 21 21 (No. 18)
>>>> CONTENTS:
>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz',
>>>> 'mtz', 'premerged', 'P 2 21 21', [34.869998931884766,
>>>> 109.19999694824219,
>>>> 135.32989501953125, 90.0, 90.0, 90.0], 2.4890134311310943, ['F1',
>>>> 'SIGF1',
>>>> 'DANO1', 'SIGDANO1']]
>>>>
>>>> File
>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz
>>>> RES: 2.5
>>>>
>>>> Guess of datafile for refinement:
>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz
>>>>
>>>> Using
>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz
>>>> for refinement
>>>>
>>>> Specify
>>>> input_refinement_file=/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz
>>>> to change this
>>>>
>>>> HKLIN ENTRY:
>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz
>>>>
>>>> FILE TYPE ccp4_mtz
>>>>
>>>> COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re',
>>>> 'SIGF_107_2re',
>>>> 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)',
>>>> 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re',
>>>> 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)']
>>>>
>>>> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1',
>>>> 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90)
>>>> Space
>>>> group: P 2 21 21 (No. 18) CONTENTS:
>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz',
>>>> 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344,
>>>> 108.92009735107422,
>>>> 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1',
>>>> 'SIGF1',
>>>> 'DANO1', 'SIGDANO1']]
>>>>
>>>> Inverse hand of space group: P 2 21 21 Creating sg entry from
>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz
>>>> Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21
>>>> (No.
>>>> 18) Space group name is: P 2 21 21 symbol is: p22121
>>>>
>>>> ****************************************
>>>>
>>>> AutoSol Input failed
>>>>
>>>> Need a symfile for solve
>>>>
>>>> ****************************************
>>>>
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