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Anyone knows the right database to download from the ncbi site?
The link in the rosetta tutorial is broken. I know that's the nr one, but fasta formated or
any input on this?

thank you


Tue, 2009-10-13 11:31

> Anyone knows the right database to download from the ncbi site?
> The link in the rosetta tutorial is broken. I know that's the nr one, but fasta formated or
> any input on this?
> thank you
> tiago

You can use UniRef90 from Fasta formated and you a have to run formatdb for setting up the psiblast database files. Just rename the UniRef90 fasta to nr and run

'/my/blast/installation/formatdb -o T -i nr'

David K

Mon, 2009-10-19 12:51


thanks ive had done and it worked, something to do with the index file, now it says it doesnt find the blosum65.iqj matrix, but its in the right directory. i just copied nnmake_database to my directory. does the script need more data from the fragments directory in rosetta.

Tue, 2009-10-20 08:08

Hi Tiago

Where did you download nnmake_database?

In the tutorial page it says provided with the release but I dont see anywhere?

I have difficulty to modify the script as I dont find following database and ss prediction software sam?

# nnmake
my $VALL = "$scratch/$fragsDir/nnmake_database";          # dir containing vall database (cvs repository 'nnmake_database')
my $VALL2 = "$scratch/$fragsDir/nnmake_database";             # alt dir containing vall database (cvs repository 'nnmake_database')
my $VALL_NAME = "vall.dat.2006-05-05";                 # filename of vall (vall.dat.<id> and vall_cst_coord.dat.<id> must exist)
my $NNMAKE = $pathToDemo."scripts/frags/";                         # nnmake binary  (cvs respository 'nnmake')
my $TRIMLOOPS = "$scratch/$fragsDir/nnmake/";                  # (cvs respository 'nnmake')

# chemshift
my $CHEMSHIFT = "$scratch/$fragsDir/chemshift/pCHEMSHIFT.gnu";     # chemshift binary (cvs repository 'chemshift')
my $TALOS_DB = "$scratch/$fragsDir/chemshift_database";                          # TALOS databases directory (cvs respository 'chemshift_database')

# jufo (secondary structure prediction software)
my $JUFO = "$scratch/src/jufo/molecule.exe";                              # jufo executable

# sam (secondary structure prediction software)
my $SAM_target99                = "$scratch/src/sam3.5.i686-linux/bin/target99";        # sam target99 executable
my $SAM_uniqueseq               = "$scratch/src/sam3.5.i686-linux/bin/uniqueseq";       # sam uniqueseq executable
my $SAM_predict_2nd_dir         = "$scratch/src/sam.predict-2nd/";                      # sam predict-2nd directory
my $SAM_predict_2nd             = "$scratch/src/sam.predict-2nd/predict-2nd";   # sam predict-2nd executable

Can anyone help me running

I also dont know what is the directory name: $fragsDir = "rosetta/rosetta_fragments_latest";

as I dont know anything about perl script does this means we create a directory and give path like this?


kind regards


Fri, 2021-09-10 08:14
G Mustafa



I am trying to use following link to generate fragments

but I cant find the nnmake_database given in the link. Can anyone share the correct link? and also help in running the as it fails to run due to failure of nr database download. However, if I select uniref96 it downloads correctly.

kind regards


Fri, 2021-09-10 05:36
G Mustafa

I am not familar with the Perl script described or fragments stuff in general, but I thought I'd mention that one can do this easily with PyRosetta too.

pose = pyrosetta.pose_from_file('****.pdb')
confragset = pyrosetta.rosetta.core.fragment.ConstantLengthFragSet(3)
pyrosetta.rosetta.core.fragment.steal_constant_length_frag_set_from_pose(pose, confragset)
print(f'{filename}: {confragset.nr_frames()} frames')
fragio = pyrosetta.rosetta.core.fragment.FragmentIO()
fragio.write_data('***.frags', confragset)

The pose can have ligands (not sure about DNA), but true to `ignore_unrecognized_res` and false to `load_PDB_components` in the init would seem wise.

The output is something like the following, which I belive the same as normal fragment files.

FRAME    1   3
         1     0 no_pdb BBTorsion S L      0.000   125.451   179.413
         2     0 no_pdb BBTorsion S E   -158.982   169.226   179.818
         3     0 no_pdb BBTorsion F E    -85.818   153.494   174.140

This works fine within PyRosetta. Although, one can use them without wasting time writing to disk, but often its via a vector of it, eg.

fragsets = pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t(1)
fragsets[1] = confragset

## Example: Threading
align = pyrosetta.rosetta.core.sequence.read_aln(format='grishin', filename='***.grishin')
threader = pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover(align=align[1], template_pose=template_pose)


Wed, 2021-09-29 01:58