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