Hi，i want to use fragment_picker to get 3-mer and 9-mer fragment,with only .fasta and .psipred.Cause i do not have pdb file ,i remove the -in::file::s .pdb
When i run fragment_picker,it tell me "can not read a referrence file"
I want to know how to solve this,thank you
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Hello,
Could you prove a more exact error message, and the exact command line you used?
We generally recommend running fragment_picker via make_fragments.pl in the tools/fragments directory.
Hello.
my error message:
caught exception
File: src/protocols/frag_picker/scores/FragmentCrmsd.cc:258
[ ERROR ] UtilityExitException
ERROR: Can't read a reference structure. Provide it with in::file::s flag
my conmand line:
:~/download/rosetta_src/demos/public/fragment_picking/BestFragmentsProtocol$ /home/advanced/download/rosetta_src/main/source/bin/fragment_picker.linuxgccrelease @flags
and the flags file:
# Input databases
#-in::file::vall <Path to vall database>
# Query-related input files
#-in::file::checkpoint input_files/2jsvX.checkpoint
-in::file::fasta input_files/2jsvX.fasta
#-in::file::s input_files/2jsvX.pdb
-frags::ss_pred input_files/2jsvX.psipred.ss2 predA
# Weights file
-frags::scoring::config input_files/simple.wghts
# What should we do?
#-frags::bounded_protocol
# three-mers only, please
-frags::frag_sizes 3
-frags::n_candidates 200
-frags::n_frags 200
# Output
-out::file::frag_prefix output_files/frags
#-frags::describe_fragments output_files/frags.fsc
-in::file::vall /home/advanced/download/rosetta_src/main/database/sampling/filtered.vall.dat.2006-05-05.gz
referrence:
https://www.rosettacommons.org/demos/latest/public/fragment_picking/README
It do not ask for a native pdb for necessary but i got a error