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

Tue Feb 2 07:32:06 PST 2010

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That said:  it sounds like you may be pointing at an out-of-date 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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