[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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