sequence file error in phenix map-to-model
Hi, I am getting an error with the sequence file attached. Could you please tell me what's wrong with this file? The error is enclosed below: Starting phenix on Mon Dec 20 11:45:46 2021 by rdey =============================================================================== Processing files: ------------------------------------------------------------------------------- Found phil, /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found real_map, /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc Files not used by program: -------------------------- /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" default_real_map = "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" phil_files = "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" default_phil = "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" } input_files { map_file = /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc seq_file = /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt ncs_file = /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec } reconstruction_symmetry { symmetry = """D2""" } control { nproc = 2 } job_title = """D41-st-Trx-19Dec21""" Starting job =============================================================================== Validating inputs Thanks a lot for your time. Regards, Raja
Sorry, the error message is
D41-st-Trx-sequence.txt is not a known sequence type.
Can someone help solving this problem?
Best regards,
Raja
On Mon, Dec 20, 2021 at 12:02 PM Raja Dey
Hi, I am getting an error with the sequence file attached. Could you please tell me what's wrong with this file? The error is enclosed below: Starting phenix on Mon Dec 20 11:45:46 2021 by rdey
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found phil, /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding PHIL files: ------------------
/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff
Processing files from PHIL:
-------------------------------------------------------------------------------
Found real_map, /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc
Files not used by program: -------------------------- /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec
Final processed PHIL parameters:
------------------------------------------------------------------------------- data_manager { real_map_files = "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" default_real_map = "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" phil_files = "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" default_phil = "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" } input_files { map_file = /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc seq_file = /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt ncs_file = /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec } reconstruction_symmetry { symmetry = """D2""" } control { nproc = 2 } job_title = """D41-st-Trx-19Dec21"""
Starting job
=============================================================================== Validating inputs
Thanks a lot for your time. Regards, Raja
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Raja Dey