[phenixbb] sequence file error in phenix map-to-model
Raja Dey
rddey80 at gmail.com
Mon Dec 20 10:02:25 PST 2021
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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> HistagTrxTEV
MGSSHHHHHHGTSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQ
NPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAGTDYDIPTTENLYFQGHM
> UBA
DVLLSMGFPRARAQKALASTGGRSVQAACDWLFSH
> PDE
VGDPFLDDPLPREYVLYLRPTGPLAQKLSDFWQQSKQICGKNKAHNIFPHITLCQFFMCEDSKVDALGEALQTTV
SRWKCKFSAPLPLELYTSSNFIGLFVKEDSAEVLKKFAADFAAEAASKTEVHVEPHKKQLHVTLAYHFQASHLPT
LEKLAQNIDVKLGCDWVATIFSRDIRFAN
> SH3
HETLQVIYPYTPQNDDELELVPGDFIFMSPMEQTSTSEGWIYGTSLTTGCSGLLPENYITKA
> NoDomain
ENYITKADECSTWIFHGSYSILNTSSSNSLTFGDGVLERRPYEDQGLGETTPLTIICQPMQPLRVNSQPGPQKRC
> HP
LFVCRHGERMDVVFGKYWLSQCFDAKGRYIRTNLNMPHSLPQRSGGFRDYEKDAPITVFGCMQARLVGEALLESN
TIIDHVYCSPSLRCVQTAHNILKGLQQENHLKIRVEPGLFEWTKWVAGSTLPAWIPPSELAAANLSVDTTYRPHI
PISKLVVSESYDTYISRSFQVTKEIISECKSKGNNILIVAHASSLEACTCQLQGLSPQNSKDF
> DimDomain
VQMVRKIPYLGFCSCEELGETGIWQLTDPPILPLTHGPTGGFNWRETLLQE
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