Summary: capra-eval is a handy utility for
comparing a model built by TEXTALTM with a true structure (if known).
Essentially, it pairs up nearest atoms between the two structures,
reports the matches it makes (and those that remain unmatched), and
then computes an RMSD (root-mean-sequare distance) between the matched
atoms, enabling the goodness of a model to be assessed.
Comments: If an atom in one model does not have a unique
neighbor in the other model within a cutoff of 3.0Å, then it is left
unassigned and excluded from the RMSD calculation. This makes the
RMSD value less sensitive to being skewed by "over-hanging" or
un-matched regions. Obviously, capra-eval only works if
you have a model of the true structure, for example, when running
tests on TEXTALTM with a protein whose structure is already known.
Usage: capra-eval -a|-c <textal-model> <true-structure>
Command-line arguments:
Explanation of Output:
The output of capra-eval contains the following information:
57 tropical> trim-chains ../capra/czra/czra-chains.pdb ../capra/czra.pdb # command line: # capra-eval czra1-imp5.pdb czra1.pdb # # Date:Fri Aug 17 13:04:49 2001 # # Compilation options: # COMPRESSED_MAPS # # !textal global parameters # 0 ! mode (see textal.h for settings) # 1 ! Seed for RNG. If non-zero, seed with this, otherwise use time. # 4 ! number of radii # 3.000000 ! radius 1 # 4.000000 ! radius 2 # 5.000000 ! radius 3 # 6.000000 ! radius 4 # 0 ! should we peakmatch (0/1)? # 9 ! integer, number of peaks to use in peak-matching # 5.000000 ! float, radius to use for density correlation calculations # 0.700000 ! float, CC, good correlation cutoff (0.7) # 400 ! int, K: number of top features to calc correlations on # 0 ! int, connected should we use only connected density(0/1)? # 1 !use sidechain axis method for CC calculations? # 0 !use error_correcting CC? # !end textal global parameters # CA 14 in CAPRA model matches CA 49 in true struct, dist=0.143221 LEU LEU $ CA 69 in CAPRA model matches CA 17 in true struct, dist=0.148825 THR THR $ CA 70 in CAPRA model matches CA 18 in true struct, dist=0.155348 SER GLU $ CA 51 in CAPRA model matches CA 90 in true struct, dist=0.166043 ARG MET $ CA 71 in CAPRA model matches CA 19 in true struct, dist=0.173582 ILE ILE $ CA 67 in CAPRA model matches CA 15 in true struct, dist=0.180827 ILE ARG $ CA 18 in CAPRA model matches CA 53 in true struct, dist=0.1826 GLU GLN $ CA 68 in CAPRA model matches CA 16 in true struct, dist=0.191828 THR VAL $ CA 25 in CAPRA model matches CA 60 in true struct, dist=0.191938 ASN LEU $ CA 82 in CAPRA model matches CA 29 in true struct, dist=0.195699 THR ILE $ CA 34 in CAPRA model matches CA 69 in true struct, dist=0.20645 THR VAL $ CA 52 in CAPRA model matches CA 91 in true struct, dist=0.233409 VAL LEU $ CA 73 in CAPRA model matches CA 21 in true struct, dist=0.247099 LYS LYS $ CA 20 in CAPRA model matches CA 55 in true struct, dist=0.248034 LEU ASN $ CA 72 in CAPRA model matches CA 20 in true struct, dist=0.267033 ALA PHE $ CA 64 in CAPRA model matches CA 12 in true struct, dist=0.271284 SER THR $ CA 23 in CAPRA model matches CA 58 in true struct, dist=0.276682 PHE HIS $ CA 35 in CAPRA model matches CA 70 in true struct, dist=0.28461 VAL LYS $ CA 22 in CAPRA model matches CA 57 in true struct, dist=0.285651 THR SER $ CA 10 in CAPRA model matches CA 45 in true struct, dist=0.294118 VAL ILE $ CA 21 in CAPRA model matches CA 56 in true struct, dist=0.296282 VAL VAL $ CA 74 in CAPRA model matches CA 22 in true struct, dist=0.302792 ALA ALA $ CA 86 in CAPRA model matches CA 33 in true struct, dist=0.305709 VAL GLU $ CA 84 in CAPRA model matches CA 31 in true struct, dist=0.310475 VAL ILE $ CA 53 in CAPRA model matches CA 92 in true struct, dist=0.310539 ALA LYS $ CA 8 in CAPRA model matches CA 43 in true struct, dist=0.31382 ALA GLY $ CA 32 in CAPRA model matches CA 67 in true struct, dist=0.316397 LEU HIS $ CA 83 in CAPRA model matches CA 30 in true struct, dist=0.320017 LYS ARG $ CA 24 in CAPRA model matches CA 59 in true struct, dist=0.323953 VAL GLN $ CA 19 in CAPRA model matches CA 54 in true struct, dist=0.325659 SER SER $ CA 81 in CAPRA model matches CA 28 in true struct, dist=0.327022 SER ARG $ CA 33 in CAPRA model matches CA 68 in true struct, dist=0.344496 ILE LEU $ CA 75 in CAPRA model matches CA 23 in true struct, dist=0.353048 LEU LEU $ CA 56 in CAPRA model matches CA 95 in true struct, dist=0.359246 VAL ILE $ CA 85 in CAPRA model matches CA 32 in true struct, dist=0.363176 GLN MET $ CA 13 in CAPRA model matches CA 48 in true struct, dist=0.363553 VAL GLN $ CA 2 in CAPRA model matches CA 37 in true struct, dist=0.374253 ILE VAL $ CA 31 in CAPRA model matches CA 66 in true struct, dist=0.383704 ILE VAL $ CA 27 in CAPRA model matches CA 62 in true struct, dist=0.384827 SER LEU $ CA 9 in CAPRA model matches CA 44 in true struct, dist=0.395598 SER HIS $ CA 26 in CAPRA model matches CA 61 in true struct, dist=0.420359 ALA LYS $ CA 28 in CAPRA model matches CA 63 in true struct, dist=0.43851 VAL LEU $ CA 37 in CAPRA model matches CA 72 in true struct, dist=0.451946 ILE LYS $ CA 3 in CAPRA model matches CA 38 in true struct, dist=0.461032 VAL SER $ CA 54 in CAPRA model matches CA 93 in true struct, dist=0.463501 MET GLN $ CA 63 in CAPRA model matches CA 11 in true struct, dist=0.473032 LEU ASP $ CA 50 in CAPRA model matches CA 89 in true struct, dist=0.476538 VAL THR $ CA 1 in CAPRA model matches CA 36 in true struct, dist=0.483934 SER SER $ CA 87 in CAPRA model matches CA 34 in true struct, dist=0.489684 VAL LEU $ CA 7 in CAPRA model matches CA 42 in true struct, dist=0.494246 ALA VAL $ CA 36 in CAPRA model matches CA 71 in true struct, dist=0.53035 ALA ALA $ CA 66 in CAPRA model matches CA 14 in true struct, dist=0.530894 ARG GLU $ CA 62 in CAPRA model matches CA 10 in true struct, dist=0.537468 ALA THR $ CA 80 in CAPRA model matches CA 27 in true struct, dist=0.550415 ALA ASN $ CA 16 in CAPRA model matches CA 51 in true struct, dist=0.556051 ILE LEU $ CA 44 in CAPRA model matches CA 83 in true struct, dist=0.558243 LEU ASP $ CA 61 in CAPRA model matches CA 9 in true struct, dist=0.564629 ALA ASN $ CA 65 in CAPRA model matches CA 13 in true struct, dist=0.606639 VAL LEU $ CA 17 in CAPRA model matches CA 52 in true struct, dist=0.627004 SER SER $ CA 55 in CAPRA model matches CA 94 in true struct, dist=0.627106 LEU ALA $ CA 42 in CAPRA model matches CA 81 in true struct, dist=0.653717 SER SER $ CA 60 in CAPRA model matches CA 99 in true struct, dist=0.663103 ALA ASN $ CA 12 in CAPRA model matches CA 47 in true struct, dist=0.704399 ASP HIS $ CA 43 in CAPRA model matches CA 82 in true struct, dist=0.730131 GLU LEU $ CA 79 in CAPRA model matches CA 26 in true struct, dist=0.736839 LEU TYR $ CA 29 in CAPRA model matches CA 64 in true struct, dist=0.779634 LEU LYS $ CA 11 in CAPRA model matches CA 46 in true struct, dist=0.784573 VAL SER $ CA 38 in CAPRA model matches CA 73 in true struct, dist=0.799915 ALA ARG $ CA 30 in CAPRA model matches CA 65 in true struct, dist=0.845913 SER SER $ CA 45 in CAPRA model matches CA 84 in true struct, dist=0.846603 GLY ASP $ CA 41 in CAPRA model matches CA 80 in true struct, dist=0.863744 LYS TYR $ CA 15 in CAPRA model matches CA 50 in true struct, dist=0.894648 ALA ASN $ CA 88 in CAPRA model matches CA 35 in true struct, dist=0.915986 VAL LEU $ CA 57 in CAPRA model matches CA 96 in true struct, dist=0.946286 SER HIS $ CA 46 in CAPRA model matches CA 85 in true struct, dist=0.960305 VAL ILE $ CA 47 in CAPRA model matches CA 86 in true struct, dist=1.04083 ALA HIS $ CA 78 in CAPRA model matches CA 25 in true struct, dist=1.13521 LEU ASP $ CA 49 in CAPRA model matches CA 88 in true struct, dist=1.22177 ALA ALA $ CA 6 in CAPRA model matches CA 41 in true struct, dist=1.31865 VAL SER $ CA 4 in CAPRA model matches CA 39 in true struct, dist=1.32312 VAL GLU $ CA 48 in CAPRA model matches CA 87 in true struct, dist=1.53654 ALA VAL $ CA 5 in CAPRA model matches CA 40 in true struct, dist=1.65693 MET ALA $ CA 76 in CAPRA model matches CA 24 in true struct, dist=1.78613 SER GLY $ CA 59 in CAPRA model matches CA 98 in true struct, dist=1.90765 PRO ALA $ CA 58 in CAPRA model matches CA 97 in true struct, dist=2.97927 GLN HIS $ CA 40 in CAPRA model matches CA 79 in true struct, dist=5.78428 GLY ILE $ CA 39 in CAPRA model matches CA 78 in true struct, dist=5.87647 GLY MET $ rms=1.14881 (n=87) CAPRA atoms not matched... 0 77 atoms in true struct. not matched... 74 75 76 77 100 101 102 103