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Fragment Generation

Segmentation Fault in Fragment picking

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

Post Situation: 

which make_fragments.pl

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)

Post Situation: 

PSIPRED secondary structure prediction in PyRosetta

Category: 
Fragment Generation

Dear All,

I am trying to preform PSIPRED secondary structure prediction in PyRosetta. This is my code so far:

psipred = pyrosetta.rosetta.core.io.external.PsiPredInterface(' ') #<--- What goes here?
psipred.run_psipred(pose , 'blueprint') #<--- Is this correct?

I think I am close at getting it to work, but I am not there yet; what goes in the first line? (pydoc3 says the argument in the first line should be cmd: str and I don't know what that is)

Post Situation: 

The vall.jul19.2011.gz Database

Category: 
Fragment Generation

Dear All,

 

Is there a URL or FTP to download the vall.jul19.2011.gz database?

I know the database resides in {ROSETTA}//tools/fragment_tools/

But if I want to direct someone to just download the database without downloading Rosetta and uncompressing it (for example to use PyRosetta independently than Rosetta). Does a URL or FTP to download the database exists?

Post Situation: 

Fragment Picking in PyRosetta

Category: 
Fragment Generation

Dear All,

 

Is there a tutorial that can show how to preform fragment picking in PyRosetta? I want to generate fragments for many structures and I do not want to overwhelm the Robetta server, thus I want to preform it in-house.

 

Any help on how or where to start to generate fragments using PyRosetta? I found that there is a mover FragmentPicker() in  pyrosetta.rosetta.protocols.frag_picker but I do not know how to use it.

 

This is my code so far:

Post Situation: 

Fragment library (vall file) from Robetta?

Category: 
Fragment Generation

Dear all,

I am using the fragment picker for multiple peptides. The issue is that I am using a limited vall library. Is there a way to produce an updated vall library from PDB or the Robetta server? I see that Robetta fragment files are available here: http://robetta.bakerlab.org/downloads/casp/casp12/fragments/ . But is there a way to combine them into a vall file?

Thanks in advance,

Alex

Post Situation: 

short peptide fragment file generation

Category: 
Fragment Generation

Hi Rosetta users,

I was trying to generate fragment files for a short peptide (9-AA) for use in abinito FlexPepDock. I checked out the demo, but found it quite difficult to follow using make_fragments.pl. I learned from the forum that the perl script is a bit outdated and we should use either the Robetta server or the new fragment picker application.  However, Robetta doesn't seem to accept very short sequences. Could anyone advise me how to use the new fragment picker application to generate fragments for short peptides. Thanks in advance!

Post Situation: 

error--rosetta fragment‐based refinement protocol for refinement against EM density

Category: 
Fragment Generation

I am trying to use rosetta fragment‐based refinement protocol for refinement against EM density. My script is attached.

It always complaints:

Post Situation: 

fragment_picker.mpi.linuxgccrelease can't find : libsqlite3.so

Category: 
Fragment Generation

I'm sorry... I'm sure this is just something basic I overlooked but I'm not sure how this is happening since it seems that a basic component is missing....

I have Rosetta compiled with "extras = mpi" and I have OpenMPI installed.

I ran:

(mpirun --mca btl_tcp_if_exclude lo,virbr0 --hostfile hostfile -np 1 /home/starone/Public/Rosetta/main/source/bin/fragment_picker.mpi.linuxgccrelease @flags > frag.out) >& frag.err

Post Situation: 

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