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

Graeme Winter graeme.winter at googlemail.com
Tue Feb 2 05:49:11 PST 2010


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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