Hi Raja,

Try to use the file attached here. I hope it works.

On Mon, Dec 20, 2021 at 3:27 PM Raja Dey <rddey80@gmail.com> wrote:

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 <rddey80@gmail.com> wrote:

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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