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

m.b.rajasekaran at reading.ac.uk m.b.rajasekaran at reading.ac.uk
Tue Feb 2 05:38:47 PST 2010



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
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          PHENIX AutoSol  Tue Feb  2 12:37:41 2010

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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

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AutoSol Input failed

Need a symfile for solve

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