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Fragment Generation

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

Submitted by lanselibai on Fri, 2020-05-08 05:38
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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Rosetta 3 - Applications

Is there other online server for generate fragment?

Submitted by ylwang on Wed, 2020-04-01 01:39
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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Rosetta 3 - General

Is native.pdb necess for fragment_picker？

Submitted by ylwang on Thu, 2020-03-12 00:57
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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Rosetta 3 - Applications

Make error during installation of updated ncbi-blast-2.9.0+-src plus error with nr-database

Submitted by Corvin on Tue, 2019-10-01 02:04
Category: 
Fragment Generation

Dear fellows,

my recent situation with setting up the fragment generation for structure prediction ab initio consists in follow:

- It seems as if I solved my problems with version compatibility of gcc-compiler and the environment variable FRAGMENT_PICKER.

- But a problem with installation of updated make_fragments.pl and install_dependencies.pl is still remained unsolved. I carried out next actions with the ncbi-blast-2.9.0+-src package:

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Rosetta 3 - Applications

kcenters_clustering_of_fragments

Submitted by bjharris on Mon, 2019-07-01 16:16
Category: 
Fragment Generation

Hello Rosetta community,

I'm having trouble finding the fragment generation application "kcenters_clustering_of_fragments." The application is mentioned as publically available in the methods section of D.A. Silva et al (2019). De novo design of potent and selective mimics of IL-2 and IL-15. Nature. Link: https://www.nature.com/articles/s41586-018-0830-7?WT.feed_name=subjects_computational-biology-and-bioinformatics

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Rosetta 3 - Applications

make_fragments.pl

Submitted by rlwoltz on Fri, 2019-02-01 10:31
Category: 
Fragment Generation

Hi everyone,

           I wanted to let you know about a bug that I was able to fix. if you use the make_fragments.pl in the /rosetta/tools/fragments/ folder it calls another script install_dependencies.pl it calls an online script update_blastdb.pl which in the install_dependencies.pl is at this url:

 

https://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl

 

it returns a 404 error. 

 

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Rosetta 3 - General

Segmentation Fault in Fragment picking

Submitted by ashu4487 on Fri, 2018-07-06 20:47
Category: 
Fragment Generation

Hello Everyone

I am trying to generate fragments for a short peptide  (12 residues) to use them further in Flexpepdock. Following are the flag and weight files

Flag file

-in::file::vall /disk/software_sources/rosetta_bin_linux_2018.09.60072_bundle/tools/fragment_tools/vall.apr24.2008.extended.blast.gz

-in::file::fasta seq.fasta
-frags::ss_pred seq.psipred.ss2 predA
-frags::scoring:config weights.wghts
-frags::frag_sizes 3 5 9

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Rosetta 3 - Applications

which make_fragments.pl

Submitted by renedominik on Mon, 2018-06-04 08:58
Category: 
Fragment Generation

There are two different versions of make_fragments.pl, several copies under demos/ (all similar except pathes) and one under tools/fragment_tools/.

Latter seems to be more recent, as it refers to the more recent vall.jul19.2011 (which is also included in this release).

But the flexpepdock tutorial points to the version in demos/

Which to use?  (Sorry, if that is a very silly question)

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Rosetta 3 - General

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