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

[Raja Dey]

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 <sharankarade at gmail.com>
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 <rddey80 at 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 at 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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>
>
>
> --
> Sharan Karade
> Postdoc-fellow
> IBBR-UMD, 9600 Gudelsky Dr,
> Rockville
> Maryland 20850
>
>
>
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