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Is native.pdb necess for fragment_picker?

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Is native.pdb necess for fragment_picker?

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 

Post Situation: 
Thu, 2020-03-12 00:57


Could you prove a more exact error message, and the exact command line you used?

We generally recommend running fragment_picker via in the tools/fragments directory.

Thu, 2020-03-12 05:38


my error message:

caught exception

File: src/protocols/frag_picker/scores/
[ 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?

# 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



It do not ask for a native pdb for necessary but i got a error



Thu, 2020-03-12 20:42