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Fragment Generation

r_frag_quality

Category: 
Fragment Generation

Hi everyone,

I would like to assess my designs using the fragment quality metric and biased forward folding. In both cases Rosetta documentation suggests to use the r_frag_quality application. However I cannot find it in my locally compiled versions of rosetta (for example in rosetta_src_2020.08.61146_bundle). Can anybody help? 

Thanks

 

 

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Creating fragment files for proteins less than 27 aa in length

Category: 
Fragment Generation

Good day.
I'd like to make abinitio structure prediction using rosetta of some small proteins (e.g. 2jof, which length is 20 amino acids). 
Such prediction requires fragment files, which can be generated using web Robetta Server or by youself using PSI-BLAST.
However, when i tried to submit a job on Robetta there was an error:
Sequence length must be between 27 and 1000 residues
Similar restriction was described in rosetta manual dedicated fragment-files:

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make_fragments.pl error

Category: 
Fragment Generation

Hello,

I am trying to run make_fragments.pl but I get this error:

FILENAME: lig_0.fasta
Sequence: DDYLWGLEAGEGISDLFD
Running sparks for phi, psi, and solvent accessibility predictions
running psiblast for sequence: lig_0.fasta
[blastpgp] WARNING:  [000.000]  posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix

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How to concatenate the 3-mer and 9-mer files for RosettaCM?

Category: 
Fragment Generation

I am now working on a protein with multiple chains, and the total amino acids exceeds 1000. So I need to submit each chain one by one, get the individual 3-mer and 9-mer fragments, then concatenate them.

http://old.robetta.org/fragmentsubmit.jsp

The attachment is the 3-mer file. After concatenating them, do I only need to adjust these three places?

I will then use the 3-mer and 9-mer for the RosettaCM.

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Is there other online server for generate fragment?

Category: 
Fragment Generation

Hi,Is the old robetta server under maintenance now?

I want generate 3-mer and 9-mer fragment but i can not find this service in new robetta ,so i use old robetta instead.But now it seems does not work.

Does any server other than the old robetta have this function?

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Is native.pdb necess for fragment_picker?

Category: 
Fragment Generation

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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