# Fragment Generation

## 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)

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## The vall.jul19.2011.gz Database

Category:
Fragment Generation

Dear All,

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

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## 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:

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## 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?

Alex

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## 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 I learned from the forum that the perl script is a bit outdated and we should use either the Robetta server or the new fragment picker application.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!

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## 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:

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## 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

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## fragment picker does not follow dihedral constraints

Category:
Fragment Generation

Hi,

I have been try fragment_picker from Rosetta weekly build 2015_39. I want to enforce a set of dihedral restraints. So I wrote the following .cst file ():

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## Error_fragment_generation

Category:
Fragment Generation

Hi

I was running makefragments.pl for my short length peptide (sequence length 6), as a pre-requirement for abinito FlexPepDock, and I am getting the error:

Error: expected creation of t001_.200.9mers after running  "/path/to/make_fragments.pl/fragment_picker.static.linuxgccrelease @t001__picker_cmd_size9.txt -j 1'!

It was working fine before, but with two abnormalities:

a. It was generating only 3 and 9 mers(no 5 mer): so I corrected the make_fragments.pl, where in "my @fragsizes" definition "5" was missing.

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