Re: [phenixbb] sequence file error in phenix map-to-model

20 Dec 2021

      Hi Sharan,
I am getting the same error saying , 'is not a known sequence type'.
Also, please see the image enclosed below that tells how the template
sequence file should look like. I tried with/without space after '>' sign
and getting the same error message.

[image: image.png]
Any suggestion from anyone would be appreciated.
Thanks,
Raja

On Mon, Dec 20, 2021 at 3:29 PM Sharan Karade 
wrote:
...
Hi Raja,
Try to use the file attached here. I hope it works.
On Mon, Dec 20, 2021 at 3:27 PM Raja Dey  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  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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--
Sharan Karade
Postdoc-fellow
IBBR-UMD, 9600 Gudelsky Dr,
Rockville
Maryland 20850