Index of /multicom_cluster/DeepRank_db_tools/tools/modeller-9.16/examples/commands

[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[ ]1aan.seg2025-08-22 14:33 3.5K 
[ ]1cuk-a2.mrc2025-08-22 14:33 251K 
[ ]1cuk-a2.pdb2025-08-22 14:33 22K 
[ ]1cuk_1_1.pdb2025-08-22 14:33 16K 
[ ]1cuk_best.MRC2025-08-22 14:33 251K 
[ ]1cuk_init.MRC2025-08-22 14:33 251K 
[ ]1cuk_init_1.pdb2025-08-22 14:33 16K 
[ ]1fas-1.atm2025-08-22 14:33 37K 
[ ]1fas-1.rsr2025-08-22 14:33 31K 
[ ]1fas-2.rsr2025-08-22 14:33 346K 
[ ]1fas-ca.rsr2025-08-22 14:33 13K 
[ ]1fas.B2025-08-22 14:33 36K 
[ ]1fas.ca2025-08-22 14:33 4.8K 
[ ]1fas.cif2025-08-22 14:33 28K 
[ ]1fas.crd2025-08-22 14:33 33K 
[ ]1fas.dih2025-08-22 14:33 4.7K 
[ ]1fas.ini2025-08-22 14:33 36K 
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[ ]1fas.ini22025-08-22 14:33 36K 
[ ]1fas.ngh2025-08-22 14:33 4.9K 
[ ]1fas.noSS2025-08-22 14:33 36K 
[ ]1fas.psa2025-08-22 14:33 5.8K 
[ ]1fas.rsr2025-08-22 14:33 13K 
[ ]1fas.sch2025-08-22 14:33 2.4K 
[ ]1fas.sol2025-08-22 14:33 34K 
[ ]1fas.ssm2025-08-22 14:33 3.8K 
[ ]1fas_fit.pdb2025-08-22 14:33 36K 
[ ]1fdn.reg2025-08-22 14:33 29K 
[ ]1fdn.swap.atm2025-08-22 14:33 30K 
[ ]1hwa-uniprot90.prf2025-08-22 14:33 39K 
[ ]1i56A-uniprot90.prf2025-08-22 14:33 40K 
[ ]1lzdA.chn2025-08-22 14:33 381  
[ ]1v7sA-uniprot90.prf2025-08-22 14:33 40K 
[ ]2abx-join.pdb2025-08-22 14:33 85K 
[ ]2abx-renamed.pdb2025-08-22 14:33 85K 
[ ]2abx.iup2025-08-22 14:33 85K 
[ ]2abx_fit.pdb2025-08-22 14:33 43K 
[ ]2ctx.aln.pdb2025-08-22 14:33 40K 
[IMG]2ctx.fit2025-08-22 14:33 40K 
[ ]2ctx.ssm2025-08-22 14:33 4.3K 
[ ]2ctx.ssm.pdb2025-08-22 14:33 40K 
[ ]2ctx.var2025-08-22 14:33 40K 
[ ]2ctx_fit.pdb2025-08-22 14:33 40K 
[ ]2nbt-1.clr2025-08-22 14:33 39K 
[ ]2nbt-2.clr2025-08-22 14:33 39K 
[ ]2nbt.fit.pdb2025-08-22 14:33 39K 
[ ]2nbt_fit.pdb2025-08-22 14:33 39K 
[ ]3lzt-uniprot90.prf2025-08-22 14:33 43K 
[ ]EM_map.MRC2025-08-22 14:33 251K 
[ ]T3lzt-ppscan.sum2025-08-22 14:33 840  
[ ]T3lzt-ppscan_0001.ali2025-08-22 14:33 76K 
[ ]T3lzt-ppscan_0002.ali2025-08-22 14:33 76K 
[ ]T3lzt-ppscan_0003.ali2025-08-22 14:33 75K 
[ ]T3lzt-ppscan_0004.ali2025-08-22 14:33 79K 
[ ]T3lzt-uniprot90.prf2025-08-22 14:33 36K 
[TXT]add_restraint.log2025-08-22 14:33 13K 
[TXT]add_restraint.py2025-08-22 14:33 1.1K 
[TXT]align.log2025-08-22 14:33 4.7K 
[TXT]align.py2025-08-22 14:33 380  
[ ]align2d.ali2025-08-22 14:33 439  
[TXT]align2d.log2025-08-22 14:33 14K 
[ ]align2d.pap2025-08-22 14:33 649  
[TXT]align2d.py2025-08-22 14:33 1.6K 
[TXT]align3d.log2025-08-22 14:33 25K 
[TXT]align3d.py2025-08-22 14:33 1.0K 
[TXT]align_consensus.log2025-08-22 14:33 1.2K 
[ ]align_consensus.py2025-08-22 14:33 377  
[TXT]alignment_read_one.log2025-08-22 14:33 1.3K 
[TXT]alignment_read_one.py2025-08-22 14:33 768  
[TXT]all_hydrogen.log2025-08-22 14:33 9.7K 
[TXT]all_hydrogen.py2025-08-22 14:33 955  
[TXT]aln_append_model.log2025-08-22 14:33 8.4K 
[TXT]aln_append_model.py2025-08-22 14:33 1.0K 
[TXT]aln_to_prof.log2025-08-22 14:33 1.2K 
[TXT]aln_to_prof.py2025-08-22 14:33 401  
[ ]alntoprof.bin2025-08-22 14:33 7.9K 
[ ]alntoprof.prf2025-08-22 14:33 928  
[ ]alpha-helix.pdb2025-08-22 14:33 4.2K 
[TXT]bestCC_1cuk2025-08-22 14:33 120  
[TXT]build_model.log2025-08-22 14:33 1.3K 
[TXT]build_model.py2025-08-22 14:33 889  
[TXT]build_profile.log2025-08-22 14:33 25K 
[TXT]build_profile.py2025-08-22 14:33 1.3K 
[TXT]build_sequence.log2025-08-22 14:33 1.3K 
[TXT]build_sequence.py2025-08-22 14:33 818  
[ ]buildprofile.ali2025-08-22 14:33 2.6K 
[ ]buildprofile.prf2025-08-22 14:33 3.8K 
[TXT]c-example.c2025-08-22 14:33 3.2K 
[ ]clean_tests2025-08-22 14:33 660  
[TXT]color_aln_model.log2025-08-22 14:33 10K 
[ ]color_aln_model.pap2025-08-22 14:33 409  
[ ]color_aln_model.py2025-08-22 14:33 1.0K 
[TXT]compare_alignments.log2025-08-22 14:33 11K 
[TXT]compare_alignments.py2025-08-22 14:33 942  
[TXT]convert_sequence_db.log2025-08-22 14:33 5.8K 
[ ]convert_sequence_db.py2025-08-22 14:33 265  
[ ]define_symmetry-1.atm2025-08-22 14:33 85K 
[ ]define_symmetry-2.atm2025-08-22 14:33 85K 
[ ]define_symmetry-3.atm2025-08-22 14:33 85K 
[TXT]define_symmetry.log2025-08-22 14:33 48K 
[TXT]define_symmetry.py2025-08-22 14:33 2.3K 
[TXT]describe.log2025-08-22 14:33 4.1K 
[TXT]describe.py2025-08-22 14:33 268  
[TXT]edit_alignment.log2025-08-22 14:33 3.1K 
[TXT]edit_alignment.py2025-08-22 14:33 673  
[ ]ednf2.pap2025-08-22 14:33 840  
[TXT]em_grid_search.log2025-08-22 14:33 5.9K 
[ ]em_grid_search.py2025-08-22 14:33 540  
[TXT]expand_alignment.log2025-08-22 14:33 1.2K 
[TXT]expand_alignment.py2025-08-22 14:33 459  
[ ]extended-chain.pdb2025-08-22 14:33 4.1K 
[ ]fer1-seq.ali2025-08-22 14:33 508  
[ ]fer1.ali2025-08-22 14:33 508  
[TXT]group_restraints.log2025-08-22 14:33 8.6K 
[TXT]group_restraints.py2025-08-22 14:33 1.1K 
[TXT]id_table.log2025-08-22 14:33 4.5K 
[TXT]id_table.py2025-08-22 14:33 1.1K 
[TXT]iupac_model.log2025-08-22 14:33 2.6K 
[TXT]iupac_model.py2025-08-22 14:33 284  
[TXT]join_chains.log2025-08-22 14:33 1.2K 
[TXT]join_chains.py2025-08-22 14:33 498  
[TXT]make_chains.log2025-08-22 14:33 1.2K 
[TXT]make_chains.py2025-08-22 14:33 748  
[TXT]make_pssmdb.log2025-08-22 14:33 1.3K 
[ ]make_pssmdb.py2025-08-22 14:33 339  
[TXT]make_region.log2025-08-22 14:33 2.1K 
[TXT]make_region.py2025-08-22 14:33 889  
[TXT]make_restraints.log2025-08-22 14:33 23K 
[ ]make_restraints.py2025-08-22 14:33 928  
[TXT]make_schedule.log2025-08-22 14:33 45K 
[TXT]make_schedule.py2025-08-22 14:33 2.1K 
[TXT]make_topology_model.log2025-08-22 14:33 1.3K 
[TXT]make_topology_model.py2025-08-22 14:33 437  
[TXT]malign.log2025-08-22 14:33 1.5K 
[TXT]malign.py2025-08-22 14:33 330  
[TXT]malign3d.log2025-08-22 14:33 55K 
[ ]malign3d.py2025-08-22 14:33 811  
[TXT]mutate_selection.log2025-08-22 14:33 1.3K 
[TXT]mutate_selection.py2025-08-22 14:33 2.0K 
[TXT]orient_model.log2025-08-22 14:33 1.3K 
[TXT]orient_model.py2025-08-22 14:33 328  
[ ]overhang-1.pap2025-08-22 14:33 445  
[ ]overhang-1.pir2025-08-22 14:33 336  
[ ]overhang.ali2025-08-22 14:33 398  
[TXT]patch.log2025-08-22 14:33 9.0K 
[TXT]patch.py2025-08-22 14:33 825  
[TXT]patch_disulfides.log2025-08-22 14:33 36K 
[TXT]patch_disulfides.py2025-08-22 14:33 1.6K 
[ ]pdb95.bin2025-08-22 14:33 2.3M 
[ ]pdb95.fsa2025-08-22 14:33 1.7M 
[TXT]pick_atoms.log2025-08-22 14:33 11K 
[TXT]pick_atoms.py2025-08-22 14:33 1.7K 
[TXT]pick_hot_atoms.log2025-08-22 14:33 11K 
[TXT]pick_hot_atoms.py2025-08-22 14:33 1.2K 
[TXT]pick_restraints.log2025-08-22 14:33 25K 
[TXT]pick_restraints.py2025-08-22 14:33 791  
[TXT]ppscan.log2025-08-22 14:33 1.8K 
[TXT]ppscan.py2025-08-22 14:33 1.3K 
[ ]profiles.list2025-08-22 14:33 86  
[ ]profiles.pssm2025-08-22 14:33 63K 
[TXT]randomize_xyz.log2025-08-22 14:33 1.2K 
[TXT]randomize_xyz.py2025-08-22 14:33 493  
[TXT]read_alignment.log2025-08-22 14:33 6.7K 
[TXT]read_alignment.py2025-08-22 14:33 612  
[TXT]read_model.log2025-08-22 14:33 1.2K 
[TXT]read_model.py2025-08-22 14:33 445  
[TXT]read_profile.log2025-08-22 14:33 1.2K 
[TXT]read_profile.py2025-08-22 14:33 375  
[TXT]read_sequence_db.log2025-08-22 14:33 4.5K 
[ ]read_sequence_db.py2025-08-22 14:33 328  
[ ]readprofile.pir2025-08-22 14:33 540  
[TXT]reindex_restraints.log2025-08-22 14:33 25K 
[TXT]reindex_restraints.py2025-08-22 14:33 1.3K 
[TXT]rename_segments.log2025-08-22 14:33 1.2K 
[TXT]rename_segments.py2025-08-22 14:33 432  
[TXT]reorder_atoms.log2025-08-22 14:33 1.3K 
[TXT]reorder_atoms.py2025-08-22 14:33 366  
[TXT]rotate_dihedrals.log2025-08-22 14:33 1.3K 
[TXT]rotate_dihedrals.py2025-08-22 14:33 914  
[TXT]rotate_model.log2025-08-22 14:33 1.2K 
[TXT]rotate_model.py2025-08-22 14:33 629  
[TXT]run_tests2025-08-22 14:33 2.6K 
[TXT]secondary_structure.log2025-08-22 14:33 1.3K 
[ ]secondary_structure.py2025-08-22 14:33 885  
[ ]segmatch.A00010000.ali2025-08-22 14:33 452  
[ ]segmatch.A00020000.ali2025-08-22 14:33 452  
[ ]segmatch.A00030000.ali2025-08-22 14:33 452  
[ ]segmatch.A00040000.ali2025-08-22 14:33 452  
[ ]segmatch.A00050000.ali2025-08-22 14:33 452  
[ ]segmatch.A00060000.ali2025-08-22 14:33 452  
[ ]segmatch.A00070000.ali2025-08-22 14:33 452  
[ ]segmatch.A00080000.ali2025-08-22 14:33 452  
[ ]segmatch.A00090000.ali2025-08-22 14:33 452  
[ ]segmatch.A00100000.ali2025-08-22 14:33 452  
[ ]segmatch.A00110000.ali2025-08-22 14:33 452  
[ ]segmatch.P00010000.pap2025-08-22 14:33 543  
[ ]segmatch.P00020000.pap2025-08-22 14:33 543  
[ ]segmatch.P00030000.pap2025-08-22 14:33 543  
[ ]segmatch.P00040000.pap2025-08-22 14:33 543  
[ ]segmatch.P00050000.pap2025-08-22 14:33 543  
[ ]segmatch.P00060000.pap2025-08-22 14:33 543  
[ ]segmatch.P00070000.pap2025-08-22 14:33 543  
[ ]segmatch.P00080000.pap2025-08-22 14:33 543  
[ ]segmatch.P00090000.pap2025-08-22 14:33 543  
[ ]segmatch.P00100000.pap2025-08-22 14:33 543  
[ ]segmatch.P00110000.pap2025-08-22 14:33 543  
[ ]segmatch.dat2025-08-22 14:33 32K 
[TXT]segment_matching.log2025-08-22 14:33 5.6K 
[ ]segment_matching.py2025-08-22 14:33 698  
[ ]seqfilt.cod2025-08-22 14:33 298  
[ ]seqfilt.grp2025-08-22 14:33 1.0K 
[TXT]seqfilter.log2025-08-22 14:33 4.4K 
[ ]seqfilter.py2025-08-22 14:33 454  
[ ]sequence.ali2025-08-22 14:33 188  
[ ]sequence.pdb2025-08-22 14:33 12K 
[TXT]sequence_search.py2025-08-22 14:33 1.3K 
[ ]sequences.pir2025-08-22 14:33 39K 
[ ]shuff_seqlib_500.bin2025-08-22 14:33 55K 
[ ]shuff_seqlib_500.fsa2025-08-22 14:33 57K 
[TXT]superpose.log2025-08-22 14:33 2.5K 
[TXT]superpose.py2025-08-22 14:33 630  
[TXT]swap_atoms_in_res.log2025-08-22 14:33 4.9K 
[TXT]swap_atoms_in_res.py2025-08-22 14:33 807  
[TXT]test-cr.log2025-08-22 14:33 1.0K 
[TXT]top_heav.lib2025-08-22 14:33 116K 
[ ]toxin-expand.ali2025-08-22 14:33 1.2K 
[ ]toxin-filter.ali2025-08-22 14:33 255  
[ ]toxin-seq.ali2025-08-22 14:33 592  
[ ]toxin-seq.pap2025-08-22 14:33 569  
[ ]toxin-str.ali2025-08-22 14:33 614  
[ ]toxin-str.pap2025-08-22 14:33 806  
[ ]toxin.ali2025-08-22 14:33 741  
[ ]toxin.fasta2025-08-22 14:33 340  
[ ]toxin.mat2025-08-22 14:33 177  
[ ]toxin.pap2025-08-22 14:33 580  
[ ]toxin.prf2025-08-22 14:33 964  
[ ]toxin.princ2025-08-22 14:33 204  
[ ]toxin.var2025-08-22 14:33 1.5K 
[ ]toxin_id.mat2025-08-22 14:33 113  
[TXT]transfer_res_numb.log2025-08-22 14:33 3.4K 
[TXT]transfer_res_numb.py2025-08-22 14:33 589  
[TXT]transfer_xyz.log2025-08-22 14:33 1.6K 
[TXT]transfer_xyz.py2025-08-22 14:33 1.0K 
[ ]very-short-for-test.cod2025-08-22 14:33 120  
[TXT]write_data.log2025-08-22 14:33 5.5K 
[TXT]write_data.py2025-08-22 14:33 1.1K 
[TXT]write_pdb_xref.log2025-08-22 14:33 8.6K 
[ ]write_pdb_xref.py2025-08-22 14:33 375