Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.7 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2012 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.7-exp dom mar 10 23:17:04 UTC 2013 ** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ===============> W E L C O M E to PDBStat <================ PDBStat has become a tool able (between other things) of: a) read and interconvert between DISMAN, DYANA, PDB, DISCOVER, IMPACT b) elaborate some info about the molecule as MW, Radius of gyration, .. c) investigate the setereochemical quality of a protein by evaluating phi, psi, chi1, impropers and chirality The sequence of acts should be: 1.- read a file (coords, constr) 2.- read a sequence file (can be free format) 3.- Follow menu (calculating, writing ...) NOTE: Be aware that if you read in a constraint file you *ALWAYS* need to read a sequence file also HAVE FUN AND ENJOY !! **** For more info type `help' or `menu' **** --> ... Reading/Loading Distances file ... 125 distance records read --> ... Reading/Loading Dihedral Library .. 1119 library records read PdbStat> [rea]d [hel]p [his]tory [men]u [phi] [qui]t... PdbStat> leyendo PDB > locate_file(): file `CTR148A_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 176 MET THR ASP PHE LEU ALA GLY ILE ARG ILE VAL GLY GLU 1 > ReadCoordsPdb(): Counting models in file `CTR148A_R3_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > ReadCoordsPdb(): After scanning there is(are) 20 model(s) > ReadCoordsPdb(): what model do you want [(1 to 20) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file CTR148A_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 56920 ATOM records read from file > ReadCoordsPdb(): --> 56920 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> > calc_order_parameters(): ... Evaluating Dihedrals CHAIN .GT. SUM.GT. RES ID DIH S(phi) S(psi) S(chi1) S(chi2) S(chi3) S(chi4) S(chi5) 0.90 1.6 ----------------------------------------------------------------------------------- MET M 1 0.570 0.735 0.365 0.182 THR M 2 0.821 0.445 0.445 ASP M 3 0.779 0.936 0.663 0.928 PHE M 4 0.990 0.993 0.932 0.994 4 4 LEU M 5 0.997 0.996 0.999 1.000 5 5 ALA M 6 0.988 0.998 6 6 GLY M 7 0.996 0.993 7 7 ILE M 8 0.997 0.998 1.000 1.000 8 8 ARG M 9 0.997 0.995 0.716 0.989 0.271 0.918 1.000 9 9 ILE M 10 0.997 0.997 0.999 0.560 10 10 VAL M 11 0.998 0.997 1.000 11 11 GLY M 12 0.986 0.993 12 12 GLU M 13 0.985 0.998 0.694 0.999 0.978 13 13 ASP M 14 0.993 0.952 0.931 0.995 14 14 LYS M 15 0.887 0.884 0.421 0.620 0.998 0.995 15 ASN M 16 0.570 0.583 0.792 0.962 GLY M 17 0.261 0.949 MET M 18 0.991 0.992 0.944 0.636 0.725 18 18 THR M 19 0.986 0.990 0.999 19 19 ASN M 20 0.984 0.984 0.880 0.868 20 20 GLN M 21 0.969 0.980 0.934 0.641 0.799 21 21 ILE M 22 0.997 0.985 0.857 0.682 22 22 THR M 23 0.975 0.995 0.930 23 23 GLY M 24 0.998 0.999 24 24 VAL M 25 0.998 0.999 1.000 25 25 ILE M 26 1.000 0.998 1.000 1.000 26 26 SER M 27 0.998 0.994 0.752 27 27 LYS M 28 0.993 0.992 0.999 1.000 1.000 1.000 28 28 PHE M 29 1.000 0.798 0.998 0.998 ASP M 30 0.788 0.917 0.434 0.962 THR M 31 0.907 0.988 0.449 31 31 ASN M 32 0.987 0.961 0.621 0.834 32 32 ILE M 33 0.951 0.997 0.998 0.968 33 33 ARG M 34 0.992 0.995 0.714 0.520 0.777 0.520 1.000 34 34 THR M 35 0.999 0.996 0.999 35 35 ILE M 36 0.982 0.998 0.570 0.999 36 36 VAL M 37 0.995 0.987 0.999 37 37 LEU M 38 0.989 0.996 0.983 0.764 38 38 ASN M 39 0.993 0.993 0.935 0.535 39 39 ALA M 40 0.987 0.994 40 40 LYS M 41 0.940 0.841 0.299 0.996 0.925 0.874 41 ASP M 42 0.733 0.919 0.812 0.947 GLY M 43 0.980 0.982 43 43 ILE M 44 0.994 0.948 0.721 0.695 44 44 PHE M 45 0.970 0.999 0.999 0.999 45 45 THR M 46 0.996 0.998 1.000 46 46 CYS M 47 0.996 0.997 0.999 47 47 ASN M 48 0.997 0.999 0.709 0.930 48 48 LEU M 49 0.997 0.985 1.000 0.999 49 49 MET M 50 0.984 0.997 0.996 0.608 0.715 50 50 ILE M 51 0.994 0.994 0.763 0.962 51 51 PHE M 52 0.997 0.990 0.996 0.898 52 52 VAL M 53 0.992 0.995 1.000 53 53 LYS M 54 0.991 0.972 0.695 0.929 1.000 0.999 54 54 ASN M 55 0.969 0.990 0.135 0.599 55 55 THR M 56 0.994 0.991 0.654 56 56 ASP M 57 0.997 0.999 1.000 1.000 57 57 LYS M 58 0.998 0.997 0.720 0.599 0.795 0.859 58 58 LEU M 59 0.999 0.998 0.999 0.999 59 59 THR M 60 0.993 0.988 0.527 60 60 THR M 61 0.998 0.999 1.000 61 61 LEU M 62 0.996 0.998 0.993 0.910 62 62 MET M 63 0.999 0.998 0.933 0.993 0.552 63 63 ASP M 64 0.998 0.999 1.000 0.999 64 64 LYS M 65 0.999 0.998 1.000 1.000 0.999 1.000 65 65 LEU M 66 0.991 0.996 0.999 0.998 66 66 ARG M 67 0.995 0.992 0.793 0.997 0.855 0.891 1.000 67 67 LYS M 68 0.991 0.991 0.999 1.000 1.000 1.000 68 68 VAL M 69 0.997 0.996 1.000 69 69 GLN M 70 0.994 0.992 0.668 0.997 0.909 70 70 GLY M 71 0.992 0.993 71 71 VAL M 72 0.996 0.999 1.000 72 72 PHE M 73 0.996 0.994 0.921 0.746 73 73 THR M 74 0.991 0.998 1.000 74 74 VAL M 75 0.997 0.993 1.000 75 75 GLU M 76 0.993 0.991 0.761 0.999 0.935 76 76 ARG M 77 0.989 0.986 0.290 0.997 0.399 0.724 1.000 77 77 LEU M 78 0.976 0.975 0.540 0.623 78 78 SER M 79 0.984 0.961 0.697 79 79 ASN M 80 0.957 0.972 0.932 0.935 80 80 LEU M 81 0.989 0.989 0.978 0.718 81 81 GLU M 82 0.951 0.937 0.651 0.794 0.964 82 82 HIS M 83 0.927 0.644 0.603 0.597 HIS M 84 0.540 0.650 0.573 0.259 HIS M 85 0.802 0.343 0.243 0.190 HIS M 86 0.645 0.627 0.534 0.681 HIS M 87 0.773 0.411 0.580 0.334 HIS M 88 0.945 0.463 0.871 0.779 MET M 99 0.480 0.570 0.736 0.365 0.182 THR M 100 0.821 0.445 0.445 ASP M 101 0.779 0.936 0.663 0.928 PHE M 102 0.990 0.993 0.932 0.994 102 102 LEU M 103 0.997 0.996 0.999 1.000 103 103 ALA M 104 0.988 0.998 104 104 GLY M 105 0.996 0.993 105 105 ILE M 106 0.997 0.998 1.000 1.000 106 106 ARG M 107 0.997 0.995 0.716 0.989 0.271 0.918 1.000 107 107 ILE M 108 0.997 0.997 0.999 0.560 108 108 VAL M 109 0.998 0.997 1.000 109 109 GLY M 110 0.986 0.993 110 110 GLU M 111 0.985 0.998 0.694 0.999 0.978 111 111 ASP M 112 0.993 0.952 0.931 0.995 112 112 LYS M 113 0.887 0.884 0.421 0.620 0.998 0.995 113 ASN M 114 0.570 0.583 0.792 0.962 GLY M 115 0.261 0.949 MET M 116 0.991 0.992 0.944 0.636 0.725 116 116 THR M 117 0.986 0.990 0.999 117 117 ASN M 118 0.984 0.984 0.880 0.868 118 118 GLN M 119 0.969 0.980 0.934 0.641 0.799 119 119 ILE M 120 0.997 0.985 0.857 0.682 120 120 THR M 121 0.975 0.995 0.930 121 121 GLY M 122 0.998 0.999 122 122 VAL M 123 0.998 0.999 1.000 123 123 ILE M 124 1.000 0.998 1.000 1.000 124 124 SER M 125 0.998 0.994 0.752 125 125 LYS M 126 0.993 0.992 0.999 1.000 1.000 1.000 126 126 PHE M 127 1.000 0.798 0.998 0.998 ASP M 128 0.788 0.917 0.434 0.962 THR M 129 0.907 0.988 0.449 129 129 ASN M 130 0.987 0.961 0.621 0.834 130 130 ILE M 131 0.951 0.997 0.998 0.968 131 131 ARG M 132 0.992 0.995 0.714 0.520 0.777 0.519 1.000 132 132 THR M 133 0.999 0.996 0.999 133 133 ILE M 134 0.982 0.998 0.570 0.999 134 134 VAL M 135 0.995 0.987 0.999 135 135 LEU M 136 0.989 0.996 0.983 0.764 136 136 ASN M 137 0.993 0.993 0.935 0.535 137 137 ALA M 138 0.987 0.994 138 138 LYS M 139 0.940 0.841 0.299 0.996 0.925 0.874 139 ASP M 140 0.733 0.919 0.812 0.946 GLY M 141 0.980 0.983 141 141 ILE M 142 0.994 0.948 0.721 0.695 142 142 PHE M 143 0.970 0.999 0.999 0.999 143 143 THR M 144 0.996 0.998 1.000 144 144 CYS M 145 0.996 0.997 0.999 145 145 ASN M 146 0.997 0.999 0.709 0.930 146 146 LEU M 147 0.997 0.985 1.000 0.999 147 147 MET M 148 0.984 0.997 0.996 0.608 0.715 148 148 ILE M 149 0.994 0.994 0.763 0.962 149 149 PHE M 150 0.997 0.990 0.997 0.898 150 150 VAL M 151 0.992 0.995 1.000 151 151 LYS M 152 0.991 0.972 0.695 0.929 1.000 0.999 152 152 ASN M 153 0.969 0.990 0.135 0.599 153 153 THR M 154 0.994 0.991 0.654 154 154 ASP M 155 0.997 0.999 1.000 1.000 155 155 LYS M 156 0.998 0.997 0.720 0.600 0.795 0.860 156 156 LEU M 157 0.999 0.998 0.999 0.999 157 157 THR M 158 0.993 0.988 0.527 158 158 THR M 159 0.998 0.999 1.000 159 159 LEU M 160 0.996 0.998 0.993 0.910 160 160 MET M 161 0.999 0.998 0.932 0.993 0.552 161 161 ASP M 162 0.998 0.999 1.000 0.999 162 162 LYS M 163 0.999 0.998 1.000 1.000 0.999 1.000 163 163 LEU M 164 0.991 0.996 0.999 0.998 164 164 ARG M 165 0.995 0.992 0.793 0.997 0.855 0.891 1.000 165 165 LYS M 166 0.991 0.991 0.999 1.000 1.000 1.000 166 166 VAL M 167 0.997 0.996 1.000 167 167 GLN M 168 0.994 0.992 0.668 0.997 0.909 168 168 GLY M 169 0.992 0.993 169 169 VAL M 170 0.996 0.999 1.000 170 170 PHE M 171 0.996 0.993 0.921 0.746 171 171 THR M 172 0.991 0.998 1.000 172 172 VAL M 173 0.997 0.993 1.000 173 173 GLU M 174 0.993 0.991 0.761 0.999 0.935 174 174 ARG M 175 0.989 0.986 0.290 0.997 0.399 0.724 1.000 175 175 LEU M 176 0.976 0.975 0.540 0.623 176 176 SER M 177 0.984 0.961 0.697 177 177 ASN M 178 0.956 0.972 0.932 0.935 178 178 LEU M 179 0.989 0.989 0.978 0.718 179 179 GLU M 180 0.951 0.937 0.651 0.794 0.964 180 180 HIS M 181 0.927 0.644 0.603 0.597 HIS M 182 0.540 0.650 0.573 0.260 HIS M 183 0.802 0.343 0.243 0.190 HIS M 184 0.645 0.626 0.534 0.681 HIS M 185 0.773 0.411 0.580 0.334 HIS M 186 0.945 0.871 0.779 Ranges: 8 from: M 4 to M 14 from: M 18 to M 28 from: M 31 to M 40 from: M 43 to M 82 from: M 102 to M 112 from: M 116 to M 126 from: M 129 to M 138 from: M 141 to M 180 PdbStat> > do_average_coords(): Making average for backbone atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for backbone onto model 1 > do_average_coords(): Calc. average coordinates backbone > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 1 is: 0.637 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 2 is: 0.434 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 3 is: 0.544 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 4 is: 0.430 (*) > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 5 is: 0.979 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 6 is: 0.474 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 7 is: 0.522 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 8 is: 0.757 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 9 is: 0.659 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 10 is: 0.716 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 11 is: 0.862 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 12 is: 0.629 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 13 is: 0.841 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 14 is: 0.566 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 15 is: 0.831 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 16 is: 0.853 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 17 is: 0.848 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 18 is: 0.759 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 19 is: 0.486 > Kabsch RMSD of backbone atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 20 is: 0.779 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..14],[18..28],[31..40],[43..82],[102..112],[116..126],[129..138],[141..180], is: 0.680 > Range of RMSD values to reference struct. is 0.430 to 0.979 > do_average_coords(): Making average for heavy atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for heavy onto model 1 > do_average_coords(): Calc. average coordinates heavy > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 1 is: 1.044 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 2 is: 0.780 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 3 is: 1.122 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 4 is: 0.669 (*) > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 5 is: 1.325 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 6 is: 0.814 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 7 is: 0.902 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 8 is: 1.168 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 9 is: 1.025 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 10 is: 1.148 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 11 is: 1.272 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 12 is: 0.899 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 13 is: 1.146 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 14 is: 0.830 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 15 is: 1.257 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 16 is: 1.187 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 17 is: 1.080 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 18 is: 1.230 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 19 is: 0.868 > Kabsch RMSD of heavy atoms in res. M[4..14],M[18..28],M[31..40],M[43..82],M[102..112],M[116..126],M[129..138],M[141..180],for model 20 is: 1.222 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..14],[18..28],[31..40],[43..82],[102..112],[116..126],[129..138],[141..180], is: 1.049 > Range of RMSD values to reference struct. is 0.669 to 1.325 PdbStat> PdbStat> *END* of program detected, BYE! ...