Is native.pdb necess for fragment_picker？

[Anonymous]

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: .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 

[Anonymous]

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.

[Anonymous]

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: 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:                   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

 

 

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