[phenixbb] AUTOSOL for MAD data with error message-'Need a symfile for solve'
Thomas C. Terwilliger
terwilliger at lanl.gov
Tue Feb 2 12:14:53 PST 2010
Hi again Frank and Graeme and Mohan,
This is now fixed and should be available in tomorrow's build of PHENIX.
Most setting should now be available in Autosol (this bug only affected
Autosol, not Autobuild or any other PHENIX routines).
Thanks for pointing out the problem (and Mohan if this does not solve it
in your case, please let me know and I'll continue to fix it).
All the best,
Tom T
>> 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 That said: it sounds like you may be pointing at an out-of-date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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>>>>>>
>>>>>>
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