Re: Basic python scripts for File Manipulation

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    • #829


        I am searching for the following files :-

        File Manipulation concatenate silentfiles change the chain id of a PDB generate a silentfile from a set of PDBs create a dummy structure from a sequence of amino acids create a homology model template from a FASTA file and a homologous structure generate .coords format from native pdb (for input to cluster_info_silent.out, see below)
        molecule.exe: generate JUFO file and rename ligand atoms (with addhydrogens.inp, mdl2rosetta.inp, and pdb2mdl.inp) generate a FASTA from a PDB rename a PDB or set of PDBs to their tag names (as shown in the silentfile)
        reconstruct_PDB_by_index: generate PDBs from abinitio-format silentfile renumber the residues of a PDB sequentially, starting at 1 renumber the atoms of a PDB sequentially, starting at 1 generate PDBs from a docking silentfile


        TMalign: aligns structures based on CA-CA distances
        VMD: X-Windows molecular graphics viewer display silentfile and scorefile columns
        gnuplot: graphically display data generate a gnuplot input file to plot the score versus another field generate a quick histogram from STDIN data

        Clustering automatic clustering of an abinitio-format silentfile
        cluster_info_silent.out: fully configurable silentfile clustering cluster a set of PDBs find per-residue variation within a cluster make a dendrogram of the clusters make a contacts plot

        Can anybody tell me where can I find them ??

      • #5182

          Some of these are in “BioTools”, which is part of the wider 3.2 package (outside the code itself).

          Some of these don’t have anything to do with Rosetta; notably gnuplot and VMD, which are publically available (probably open-source) software, which you can easily find on the internet.

          You should also try looking through the 2.x releases.

          Let me know where you found this list and I’ll try to track that author down to get them to tell me where it’s supposed to be.

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