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 `SGR209C_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER PROTEIN BINDING 30-JUN-10 2L06 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE PBS LINKER POLYPEPTIDE DOMAIN (FRAGMENT > ReadCoordsPdb(): >> TITLE 2 254-400) OF PHYCOBILISOME LINKER PROTEIN APCE FROM SYNECHOCYSTIS SP. > ReadCoordsPdb(): >> TITLE 3 PCC 6803. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SGR209C > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `SGR209C_NMR_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 SGR209C_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 50340 ATOM records read from file > ReadCoordsPdb(): --> 50340 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 ----------------------------------------------------------------------------------- PRO A 1 0.619 0.988 0.923 GLN A 2 0.642 0.342 0.514 0.525 0.169 SER A 3 0.402 0.430 0.355 TYR A 4 0.442 0.298 0.305 0.179 PHE A 5 0.672 0.256 0.160 0.216 ASN A 6 0.282 0.535 0.514 0.571 ALA A 7 0.759 0.412 ALA A 8 0.761 0.119 ALA A 9 0.490 0.180 LYS A 10 0.301 0.243 0.373 0.553 0.433 0.269 ARG A 11 0.359 0.546 0.455 0.574 0.344 0.816 0.998 GLN A 12 0.556 0.705 0.262 0.567 0.097 LYS A 13 0.608 0.804 0.446 0.780 0.334 0.381 TYR A 14 0.980 0.941 0.993 0.555 14 14 ALA A 15 0.973 0.988 15 15 MET A 16 0.984 0.944 0.658 0.224 0.074 16 16 LYS A 17 0.921 0.993 0.603 0.983 0.646 0.328 17 17 PRO A 18 0.996 0.876 0.954 0.884 18 GLY A 19 0.829 0.886 19 LEU A 20 0.923 0.981 0.739 0.744 20 20 SER A 21 0.983 0.991 0.650 21 21 ALA A 22 0.999 0.993 22 22 LEU A 23 0.998 0.994 0.906 0.782 23 23 GLU A 24 0.997 0.999 0.797 0.158 0.358 24 24 LYS A 25 0.999 0.998 0.779 0.925 0.717 0.808 25 25 ASN A 26 0.999 0.999 0.606 0.708 26 26 ALA A 27 0.999 0.999 27 27 VAL A 28 0.998 0.998 0.998 28 28 ILE A 29 0.999 0.997 0.998 0.774 29 29 LYS A 30 0.999 0.996 0.710 0.637 0.655 0.303 30 30 ALA A 31 0.999 0.998 31 31 ALA A 32 0.999 0.996 32 32 TYR A 33 0.997 0.990 0.992 0.893 33 33 ARG A 34 0.992 0.977 0.612 0.722 0.083 0.713 0.998 34 34 GLN A 35 0.984 0.977 0.463 0.129 0.173 35 35 ILE A 36 0.989 0.992 0.998 0.665 36 36 PHE A 37 0.979 0.963 0.997 0.897 37 37 GLU A 38 0.993 0.988 0.566 0.652 0.302 38 38 ARG A 39 0.518 0.579 0.524 0.556 0.361 0.828 0.998 ASP A 40 0.642 0.408 0.256 0.402 ILE A 41 0.680 0.871 0.928 0.953 THR A 42 0.659 0.798 0.179 LYS A 43 0.539 0.354 0.651 0.876 0.364 0.434 ALA A 44 0.299 0.859 TYR A 45 0.678 0.307 0.654 0.376 SER A 46 0.287 0.338 0.129 GLN A 47 0.499 0.904 0.423 0.497 0.246 SER A 48 0.997 0.994 0.723 48 48 ILE A 49 0.998 0.994 0.997 0.550 49 49 SER A 50 0.996 0.996 0.143 50 50 TYR A 51 0.997 0.994 0.994 0.986 51 51 LEU A 52 0.999 0.998 0.999 0.999 52 52 GLU A 53 0.998 0.996 0.927 0.826 0.270 53 53 SER A 54 0.993 0.994 0.087 54 54 GLN A 55 0.998 0.997 0.991 0.456 0.259 55 55 VAL A 56 0.997 0.997 0.999 56 56 ARG A 57 0.997 0.992 0.761 0.842 0.149 0.720 0.998 57 57 ASN A 58 0.983 0.974 0.598 0.439 58 58 GLY A 59 0.976 0.993 59 59 ASP A 60 0.995 0.995 0.770 0.622 60 60 ILE A 61 0.991 0.986 0.999 1.000 61 61 SER A 62 0.981 0.986 0.275 62 62 MET A 63 0.998 0.994 0.687 0.426 0.298 63 63 LYS A 64 0.995 0.990 0.834 0.558 0.784 0.537 64 64 GLU A 65 0.997 0.996 0.640 0.073 0.313 65 65 PHE A 66 0.999 0.997 0.998 0.994 66 66 VAL A 67 0.999 0.999 0.999 67 67 ARG A 68 0.998 0.993 0.710 0.951 0.141 0.769 0.997 68 68 ARG A 69 0.997 0.991 0.777 0.413 0.561 0.708 0.997 69 69 LEU A 70 0.996 0.995 0.997 1.000 70 70 ALA A 71 0.998 0.993 71 71 LYS A 72 0.985 0.975 0.591 0.887 0.629 0.359 72 72 SER A 73 0.992 0.994 0.573 73 73 PRO A 74 0.999 0.996 0.940 0.854 74 74 LEU A 75 0.998 0.990 0.881 0.787 75 75 TYR A 76 0.994 0.990 0.995 0.698 76 76 ARG A 77 0.990 0.989 0.604 0.859 0.490 0.730 0.999 77 77 LYS A 78 0.990 0.961 0.639 0.663 0.492 0.512 78 78 GLN A 79 0.968 0.120 0.994 0.567 0.356 PHE A 80 0.112 0.771 0.733 0.347 PHE A 81 0.839 0.967 0.997 0.900 81 GLU A 82 0.885 0.903 0.678 0.307 0.286 82 PRO A 83 0.981 0.890 0.936 0.878 83 PHE A 84 0.966 0.845 0.998 0.603 84 ILE A 85 0.897 0.977 0.452 0.797 85 ASN A 86 0.996 0.985 0.301 0.509 86 86 SER A 87 0.997 0.986 0.173 87 87 ARG A 88 0.987 0.996 0.632 0.194 0.337 0.694 0.998 88 88 ALA A 89 0.999 0.997 89 89 LEU A 90 0.999 0.997 0.997 0.999 90 90 GLU A 91 0.997 0.993 0.529 0.600 0.449 91 91 LEU A 92 0.999 0.997 0.693 0.984 92 92 ALA A 93 0.999 0.998 93 93 PHE A 94 0.999 0.992 0.958 0.318 94 94 ARG A 95 0.990 0.983 0.650 0.849 0.248 0.615 0.998 95 95 HIS A 96 0.995 0.992 0.745 0.672 96 96 ILE A 97 0.990 0.987 0.999 1.000 97 97 LEU A 98 0.975 0.983 0.948 0.831 98 98 GLY A 99 0.971 0.949 99 99 ARG A 100 0.905 0.337 0.773 0.714 0.112 0.707 0.998 GLY A 101 0.278 0.967 PRO A 102 0.991 0.958 0.947 0.870 102 102 SER A 103 0.955 0.949 0.485 103 103 SER A 104 0.927 0.969 0.362 104 104 ARG A 105 0.995 0.990 0.108 0.543 0.461 0.701 0.998 105 105 GLU A 106 0.994 0.991 0.384 0.319 0.414 106 106 GLU A 107 0.998 0.993 0.922 0.614 0.559 107 107 VAL A 108 0.999 0.998 0.999 108 108 GLN A 109 0.998 0.995 0.689 0.608 0.054 109 109 LYS A 110 0.999 0.997 0.966 0.875 0.937 0.161 110 110 TYR A 111 0.994 0.999 0.999 0.223 111 111 PHE A 112 0.999 0.999 0.997 0.996 112 112 SER A 113 0.999 0.997 0.386 113 113 ILE A 114 0.997 0.999 0.999 1.000 114 114 VAL A 115 0.999 0.998 0.999 115 115 SER A 116 0.999 0.981 0.300 116 116 SER A 117 0.987 0.992 0.140 117 117 GLY A 118 0.984 0.917 118 118 GLY A 119 0.927 0.988 119 119 LEU A 120 0.999 1.000 0.951 0.999 120 120 PRO A 121 0.999 0.995 0.946 0.856 121 121 ALA A 122 0.996 0.998 122 122 LEU A 123 0.999 0.996 0.999 0.999 123 123 VAL A 124 1.000 0.998 0.999 124 124 ASP A 125 0.998 0.995 0.660 0.396 125 125 ALA A 126 0.999 0.997 126 126 LEU A 127 0.993 0.993 0.999 1.000 127 127 VAL A 128 0.993 0.990 0.997 128 128 ASP A 129 0.984 0.941 0.743 0.784 129 129 SER A 130 0.989 0.984 0.377 130 130 GLN A 131 0.995 0.987 0.687 0.512 0.347 131 131 GLU A 132 0.997 0.994 0.489 0.401 0.353 132 132 TYR A 133 0.994 0.983 0.535 0.429 133 133 ALA A 134 0.994 0.985 134 134 ASP A 135 0.994 0.981 0.782 0.359 135 135 TYR A 136 0.987 0.982 0.823 0.352 136 136 PHE A 137 0.960 0.972 0.703 0.260 137 137 GLY A 138 0.965 0.929 138 138 GLU A 139 0.968 0.987 0.763 0.651 0.215 139 139 GLU A 140 0.987 0.981 0.612 0.810 0.313 140 140 THR A 141 0.987 0.988 0.957 141 141 VAL A 142 0.985 0.994 0.994 142 142 PRO A 143 0.970 0.928 0.928 0.881 143 143 TYR A 144 0.910 0.635 0.603 0.193 LEU A 145 0.879 0.565 0.749 0.599 ARG A 146 0.453 0.183 0.529 0.606 0.409 0.628 0.997 GLY A 147 0.250 0.341 LEU A 148 0.299 0.324 0.422 0.424 GLU A 149 0.689 0.403 0.413 0.381 0.331 HIS A 150 0.682 0.486 0.523 0.306 HIS A 151 0.501 0.191 0.419 0.137 HIS A 152 0.700 0.542 0.421 0.291 HIS A 153 0.709 0.226 0.227 0.166 HIS A 154 0.450 0.324 0.323 0.285 HIS A 155 0.791 0.360 0.292 Ranges: 5 from: A 14 to A 17 from: A 20 to A 38 from: A 48 to A 78 from: A 86 to A 99 from: A 102 to A 143 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. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 1 is: 0.787 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 2 is: 0.993 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 3 is: 0.650 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 4 is: 0.780 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 5 is: 0.850 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 6 is: 0.627 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 7 is: 0.823 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 8 is: 0.920 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 9 is: 0.802 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 10 is: 0.664 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 11 is: 0.857 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 12 is: 0.652 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 13 is: 0.587 (*) > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 14 is: 0.720 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 15 is: 0.694 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 16 is: 0.779 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 17 is: 0.772 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 18 is: 0.857 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 19 is: 0.977 > Kabsch RMSD of backbone atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 20 is: 0.822 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[14..17],[20..38],[48..78],[86..99],[102..143], is: 0.781 > Range of RMSD values to reference struct. is 0.587 to 0.993 > 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. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 1 is: 1.171 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 2 is: 1.429 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 3 is: 1.127 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 4 is: 1.308 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 5 is: 1.412 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 6 is: 1.226 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 7 is: 1.296 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 8 is: 1.349 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 9 is: 1.317 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 10 is: 1.167 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 11 is: 1.396 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 12 is: 1.072 (*) > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 13 is: 1.086 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 14 is: 1.212 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 15 is: 1.220 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 16 is: 1.256 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 17 is: 1.306 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 18 is: 1.365 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 19 is: 1.454 > Kabsch RMSD of heavy atoms in res. A[14..17],A[20..38],A[48..78],A[86..99],A[102..143],for model 20 is: 1.374 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[14..17],[20..38],[48..78],[86..99],[102..143], is: 1.277 > Range of RMSD values to reference struct. is 1.072 to 1.454 PdbStat> PdbStat> *END* of program detected, BYE! ...