rna_calc_rmsd.py ------------------------------------------------------------------------------- Using PyMOL align: ./rna_calc_rmsd.py -m align -t test_data/struc1.pdb -o test_output/rmsd_calc_dir_to_target.tsv test_data/struc1.pdb test_data/struc2.pdb test_data/struc3.pdb test_data/struc4.pdb rmsd_calc_rmsd_to_target -------------------------------------------------------------------------------- method: align # of models: 4 struc1.pdb 0.0 1321 struc2.pdb 11.8030576706 1321 struc3.pdb 4.87882900238 1321 struc4.pdb 3.98158359528 1321 # of atoms used: 1321 csv was created! test_output/rmsd_calc_dir_to_target.tsv or by default full atom rmsd with the internal lib: $ ./rna_calc_rmsd.py -t test_data/struc1.pdb -o test_output/rmsd_calc_dir_to_target.tsv test_data/struc1.pdb test_data/struc2.pdb test_data/struc3.pdb test_data/struc4.pdb rmsd_calc_rmsd_to_target -------------------------------------------------------------------------------- # of models: 4 target:struc1.pdb rmsd_all struc1.pdb 0.0 struc2.pdb 11.803 struc3.pdb 4.879 struc4.pdb 3.982 tsv was created! test_output/rmsd_calc_dir_to_target.tsv .. select some residues and ignore some atoms $ ./rna_calc_rmsd.py -t test_data/pistol/5k7c_clean_onechain_renumber_as_puzzle_srr.pdb --target_selection A:1-47+52-62 --model_selection A:1-47+52-62 /Users/magnus/work/src/rna-pdb-tools/rna_pdb_tools/utils/rna_calc_rmsd/test_data/pistol/clusters/pistol_thrs0.50A_clust01-000001_AA.pdb --model_ignore_selection A/57/O2\' test_data/pistol/clusters/*_AA.pdb rmsd_calc_rmsd_to_target -------------------------------------------------------------------------------- method: # of models: 4 pistol_thrs0.50A_clust01-000001_AA.pdb 7.59648219355 1237 pistol_thrs0.50A_clust01-000001_AA.pdb 7.59648219355 1237 pistol_thrs0.50A_clust02-000001_AA.pdb 7.76647001671 1237 pistol_thrs0.50A_clust03-000001_AA.pdb 18.1711015479 1237 # of atoms used: 1237 csv was created! rmsds.csv rmsd_calc_dir.py ------------------------------------------------------------------------------- The program calculates all-atom rmsds (root-mean-square deviation) for all PDB structures in a given folder and save them to a file, as a matrix (which can be read by ). Usage: $ ./rna_calc_rmsd_all_vs_all.py -i test_data -o test_output/matrix.txt calc_rmsd_dir -------------------------------------------------------------------------------- # of models: 4 ... 1 test_data/struc1.pdb ... 2 test_data/struc2.pdb ... 3 test_data/struc3.pdb ... 4 test_data/struc4.pdb # test_data/struc1.pdb test_data/struc2.pdb test_data/struc3.pdb test_data/struc4.pdb 0.0 11.803 4.879 3.982 11.803 0.0 12.153 12.043 4.879 12.153 0.0 3.487 3.982 12.043 3.487 0.0 matrix was created! test_output/matrix.txt Output: $ head test_output/matrix.txt # test_data/struc1.pdb test_data/struc2.pdb test_data/struc3.pdb test_data/struc4.pdb 0.0 11.803 4.879 3.982 11.803 0.0 12.153 12.043 4.879 12.153 0.0 3.487 3.982 12.043 3.487 0.0 The program is using Biopython: Cock, P.J.A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878 The program is using (included in lib/) https://github.com/charnley/rmsd . ``` rna_calc_rmsd_multi_targets.py --models *.pdb \ --targets solutions/*.pdb \ --target-selection A:1-27+29-41 \ --model-selection A:1-27+29-41 solutions/21_solution_0_ChainA.pdb -------------------------------------------------------------------------------- # method: all-atom-built-in # of models: 60 # of atoms used: 861 csv was created! 21_solution_0_ChainA.csv solutions/21_solution_0_ChainB.pdb -------------------------------------------------------------------------------- # method: all-atom-built-in # of models: 60 # of atoms used: 861 csv was created! 21_solution_0_ChainB.csv solutions/21_solution_1_ChainA.pdb -------------------------------------------------------------------------------- # method: all-atom-built-in # of models: 60 # of atoms used: 861 csv was created! 21_solution_1_ChainA.csv solutions/21_solution_1_ChainB.pdb -------------------------------------------------------------------------------- # method: all-atom-built-in # of models: 60 # of atoms used: 861 csv was created! 21_solution_1_ChainB.csv solutions/21_solution_2.pdb -------------------------------------------------------------------------------- # method: all-atom-built-in # of models: 60 # of atoms used: 861 csv was created! 21_solution_2.csv -------------------------------------------------------------------------------- 21_solution_0_ChainA.pdb 21_solution_0_ChainB.pdb 21_solution_1_ChainA.pdb 21_solution_1_ChainB.pdb 21_solution_2.pdb mean median variance min max sd fn 21_3dRNA_1_rpr.pdb 12.17 12.11 12.17 12.11 12.11 12.13 12.11 0.00 12.11 12.17 0.03 21_3dRNA_2_rpr.pdb 12.48 12.43 12.48 12.43 12.40 12.44 12.43 0.00 12.40 12.48 0.04 21_3dRNA_3_rpr.pdb 12.04 12.05 12.04 12.05 12.13 12.06 12.05 0.00 12.04 12.13 0.04 21_3dRNA_4_rpr.pdb 18.01 17.96 18.01 17.96 18.06 18.00 18.01 0.00 17.96 18.06 0.04 21_3dRNA_5_rpr.pdb 17.61 17.49 17.61 17.49 17.57 17.55 17.57 0.00 17.49 17.61 0.06 21_Adamiak_1_rpr.pdb 4.64 4.61 4.64 4.61 4.64 4.63 4.64 0.00 4.61 4.64 0.02 21_Adamiak_2_rpr.pdb 4.65 4.62 4.65 4.62 4.64 4.64 4.64 0.00 4.62 4.65 0.02 21_Adamiak_3_rpr.pdb 4.61 4.58 4.61 4.58 4.58 4.59 4.58 0.00 4.58 4.61 0.02 21_Adamiak_4_rpr.pdb 4.58 4.51 4.58 4.51 4.54 4.54 4.54 0.00 4.51 4.58 0.04 21_Adamiak_5_rpr.pdb 5.50 5.56 5.50 5.56 5.56 5.54 5.56 0.00 5.50 5.56 0.03 21_Bujnicki_1_rpr.pdb 6.77 6.77 6.77 6.77 6.78 6.77 6.77 0.00 6.77 6.78 0.00 21_Bujnicki_2_rpr.pdb 8.69 8.84 8.69 8.84 8.79 8.77 8.79 0.01 8.69 8.84 0.08 21_Bujnicki_3_rpr.pdb 11.98 11.97 11.98 11.97 12.20 12.02 11.98 0.01 11.97 12.20 0.10 21_Bujnicki_4_rpr.pdb 6.44 6.39 6.44 6.39 6.41 6.41 6.41 0.00 6.39 6.44 0.03 21_Bujnicki_5_rpr.pdb 21.56 21.54 21.56 21.54 21.69 21.58 21.56 0.00 21.54 21.69 0.06 21_ChenHighLig_1_rpr.pdb 4.01 3.97 4.01 3.97 4.07 4.01 4.01 0.00 3.97 4.07 0.04 21_ChenHighLig_2_rpr.pdb 3.79 3.75 3.79 3.75 3.71 3.76 3.75 0.00 3.71 3.79 0.03 21_ChenHighLig_3_rpr.pdb 5.08 4.95 5.08 4.95 5.01 5.01 5.01 0.00 4.95 5.08 0.07 21_ChenHighLig_4_rpr.pdb 4.59 4.59 4.59 4.59 4.65 4.60 4.59 0.00 4.59 4.65 0.03 21_ChenHighLig_5_rpr.pdb 7.00 6.97 7.00 6.97 6.96 6.98 6.97 0.00 6.96 7.00 0.02 21_ChenLowLig_1_rpr.pdb 4.01 3.97 4.01 3.97 4.07 4.01 4.01 0.00 3.97 4.07 0.04 21_ChenLowLig_2_rpr.pdb 3.79 3.75 3.79 3.75 3.71 3.76 3.75 0.00 3.71 3.79 0.03 21_ChenLowLig_3_rpr.pdb 5.08 4.95 5.08 4.95 5.01 5.01 5.01 0.00 4.95 5.08 0.07 21_ChenLowLig_4_rpr.pdb 4.59 4.59 4.59 4.59 4.65 4.60 4.59 0.00 4.59 4.65 0.03 21_ChenLowLig_5_rpr.pdb 7.00 6.97 7.00 6.97 6.96 6.98 6.97 0.00 6.96 7.00 0.02 21_DasLORES_1_rpr.pdb 4.24 4.10 4.24 4.10 4.10 4.16 4.10 0.01 4.10 4.24 0.08 21_DasLORES_2_rpr.pdb 4.51 4.45 4.51 4.45 4.49 4.48 4.49 0.00 4.45 4.51 0.03 21_DasLORES_3_rpr.pdb 14.46 14.26 14.46 14.26 14.42 14.37 14.42 0.01 14.26 14.46 0.10 21_DasLORES_4_rpr.pdb 6.39 6.43 6.39 6.43 6.50 6.43 6.43 0.00 6.39 6.50 0.04 21_DasLORES_5_rpr.pdb 8.92 8.98 8.92 8.98 9.16 8.99 8.98 0.01 8.92 9.16 0.10 21_Das_1_rpr.pdb 5.71 5.60 5.71 5.60 5.61 5.65 5.61 0.00 5.60 5.71 0.06 21_Das_2_rpr.pdb 5.53 5.42 5.53 5.42 5.44 5.47 5.44 0.00 5.42 5.53 0.06 21_Das_3_rpr.pdb 5.07 5.06 5.07 5.06 5.01 5.05 5.06 0.00 5.01 5.07 0.03 21_Das_4_rpr.pdb 5.73 5.57 5.73 5.57 5.61 5.64 5.61 0.01 5.57 5.73 0.08 21_Das_5_rpr.pdb 6.04 6.01 6.04 6.01 6.13 6.05 6.04 0.00 6.01 6.13 0.05 21_RNAComposer_1_rpr.pdb 14.79 14.70 14.79 14.70 14.69 14.73 14.70 0.00 14.69 14.79 0.05 21_RNAComposer_2_rpr.pdb 18.32 18.14 18.32 18.14 18.24 18.23 18.24 0.01 18.14 18.32 0.09 21_RNAComposer_3_rpr.pdb 12.30 12.12 12.30 12.12 12.26 12.22 12.26 0.01 12.12 12.30 0.09 21_RNAComposer_4_rpr.pdb 13.24 12.99 13.24 12.99 13.13 13.12 13.13 0.02 12.99 13.24 0.13 21_RNAComposer_5_rpr.pdb 17.03 16.94 17.03 16.94 17.02 16.99 17.02 0.00 16.94 17.03 0.05 21_RW3D_1_rpr.pdb 18.10 17.85 18.10 17.85 18.01 17.98 18.01 0.02 17.85 18.10 0.13 21_RW3D_2_rpr.pdb 16.29 16.06 16.29 16.06 16.19 16.18 16.19 0.01 16.06 16.29 0.12 21_RW3D_3_rpr.pdb 17.91 17.73 17.91 17.73 17.87 17.83 17.87 0.01 17.73 17.91 0.09 21_RW3D_4_rpr.pdb 18.38 18.14 18.38 18.14 18.29 18.27 18.29 0.01 18.14 18.38 0.12 21_RW3D_5_rpr.pdb 18.29 18.05 18.29 18.05 18.21 18.18 18.21 0.01 18.05 18.29 0.12 21_RW3D_6_rpr.pdb 16.98 16.86 16.98 16.86 16.96 16.93 16.96 0.00 16.86 16.98 0.06 21_RW3D_7_rpr.pdb 18.27 18.01 18.27 18.01 18.17 18.15 18.17 0.02 18.01 18.27 0.13 21_RW3D_8_rpr.pdb 17.83 17.60 17.83 17.60 17.75 17.72 17.75 0.01 17.60 17.83 0.12 21_RW3D_9_rpr.pdb 18.15 17.93 18.15 17.93 18.08 18.05 18.08 0.01 17.93 18.15 0.11 21_RW3D_10_rpr.pdb 16.20 16.08 16.20 16.08 16.18 16.15 16.18 0.00 16.08 16.20 0.06 21_Sanbonmatsu_1_rpr.pdb 14.84 14.61 14.84 14.61 14.73 14.73 14.73 0.01 14.61 14.84 0.12 21_Sanbonmatsu_2_rpr.pdb 14.84 14.61 14.84 14.61 14.73 14.73 14.73 0.01 14.61 14.84 0.12 21_Sanbonmatsu_3_rpr.pdb 13.95 14.11 13.95 14.11 14.13 14.05 14.11 0.01 13.95 14.13 0.09 21_Sanbonmatsu_4_rpr.pdb 13.95 14.11 13.95 14.11 14.13 14.05 14.11 0.01 13.95 14.13 0.09 21_simRNA_1_rpr.pdb 11.88 11.88 11.88 11.88 12.10 11.92 11.88 0.01 11.88 12.10 0.10 21_simRNA_2_rpr.pdb 11.58 11.55 11.58 11.55 11.71 11.59 11.58 0.00 11.55 11.71 0.07 21_simRNA_3_rpr.pdb 13.15 13.15 13.15 13.15 13.36 13.19 13.15 0.01 13.15 13.36 0.09 21_simRNA_4_rpr.pdb 10.65 10.65 10.65 10.65 10.75 10.67 10.65 0.00 10.65 10.75 0.04 21_simRNA_5_rpr.pdb 13.15 13.15 13.15 13.15 13.36 13.19 13.15 0.01 13.15 13.36 0.09 21_solution_2_rpr.pdb 0.87 0.90 0.87 0.90 0.00 0.71 0.87 0.16 0.00 0.90 0.40 -------------------------------------------------------------------------------- Save rna_calc_rmsd_multi_targets_output.csv ```