- This topic has 3 replies, 3 voices, and was last updated 12 years ago by Anonymous.
November 15, 2011 at 9:20 pm #1085Anonymous
I would like to generate a fragment library based on a sequence. I tried running the fragment_picker demos in rosetta3.3/rosetta_demos/fragment_picker and it seems I need to include a pdb and also psipred (.ss2) file. The documentation seems to say that only vall .fasta .wghts are mandatory. I only have sequence — can I still run this protocol?
I think if I don’t have any third party secondary structure information or a pdb I somehow need to change the .wghts file. For instance the .wghts given in the demo reference predA (BestFragmentsProtocol/input_files/simple.wghts) or psipred, sam, jufo (QuotaProtocol/input_files/quota-protocol.wghts).
November 15, 2011 at 9:26 pm #6266Anonymous
A) You can try changing the weights to zero in the weights files you mention. There should be a real-number-valued column to change to zero (or try deleting those rows). I don’t know which weight to leave on for sequence-only prediction; play around or maybe it’s in the documentation?
You can create dummy secondary structure prediction (all loop, if you prefer) and run with that?
November 15, 2011 at 9:46 pm #6267Anonymous
> it seems I need to include a pdb and also psipred (.ss2) file.
You need to provide the query amino acid sequence. It may come in the form of FASTA file, PsiBlast checkpoint or a PDB file. psipred file is not required. Assuming that you have only the FASTA file, your weights file would look as follows:
RamaScore 150 2.0 -
SequenceSimilarity 200 2.0 -
and your flag file:
-frags:frag_sizes 9 3
Note, that without secondary structure prediction, you can’t use the quota protocol
November 19, 2011 at 12:03 am #6278Anonymous
Thanks! I got it working… the only change that SequenceSimilarity is not recognized as a score type. Perhaps you meant SecondarySimilarity – but this doesn’t seem to work with just a fasta file. In the end I generated some fragments with this *wghts file:
RamaScore 150 2.0 -
Robetta (which isn’t as flexible as fragment_picker) generates the .jufo_ss, .psipred, and .psipred_ss2 files which can be used this fragment_picker protocol
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