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 `SRR115C_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 29-DEC-08 2KCV > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF TETRATRICOPEPTIDE REPEAT DOMAIN > ReadCoordsPdb(): >> TITLE 2 PROTEIN SRU_0103 FROM SALINIBACTER RUBER, NORTHEAST > ReadCoordsPdb(): >> TITLE 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET SRR115C > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `SRR115C_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 SRR115C_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 31340 ATOM records read from file > ReadCoordsPdb(): --> 31340 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 ----------------------------------------------------------------------------------- GLU A 1 0.450 0.337 0.259 0.325 ASP A 2 0.887 0.977 0.467 0.146 2 PRO A 3 0.981 0.965 0.906 0.851 3 3 GLU A 4 0.982 0.986 0.997 0.520 0.281 4 4 ASP A 5 0.997 0.997 0.548 0.288 5 5 PRO A 6 0.997 0.995 0.922 0.838 6 6 PHE A 7 0.999 0.998 0.996 0.899 7 7 THR A 8 0.996 0.996 0.995 8 8 ARG A 9 1.000 1.000 0.996 0.950 0.874 0.763 0.996 9 9 TYR A 10 0.999 0.999 0.997 0.997 10 10 ALA A 11 0.998 0.999 11 11 LEU A 12 0.999 0.998 0.999 0.998 12 12 ALA A 13 0.999 0.999 13 13 GLN A 14 0.999 0.998 0.999 0.996 0.603 14 14 GLU A 15 0.998 0.998 0.996 0.480 0.520 15 15 HIS A 16 0.999 0.998 0.997 0.963 16 16 LEU A 17 0.999 0.996 0.999 0.999 17 17 LYS A 18 0.998 0.995 0.550 0.993 0.218 0.594 18 18 HIS A 19 0.997 0.993 0.993 0.638 19 19 ASP A 20 0.998 0.988 0.929 0.905 20 20 ASN A 21 0.998 0.996 0.995 0.907 21 21 ALA A 22 0.999 0.998 22 22 SER A 23 0.999 0.995 0.359 23 23 ARG A 24 0.998 0.999 0.992 0.997 0.999 0.926 1.000 24 24 ALA A 25 1.000 0.999 25 25 LEU A 26 1.000 0.999 0.999 0.999 26 26 ALA A 27 0.999 0.999 27 27 LEU A 28 0.999 0.997 0.996 0.997 28 28 PHE A 29 0.999 0.999 0.999 0.999 29 29 GLU A 30 0.998 0.996 0.999 0.998 0.459 30 30 GLU A 31 0.998 0.996 0.930 0.665 0.748 31 31 LEU A 32 0.999 0.996 0.989 0.998 32 32 VAL A 33 0.998 0.999 0.999 33 33 GLU A 34 0.998 0.995 0.999 0.997 0.246 34 34 THR A 35 0.994 0.998 0.688 35 35 ASP A 36 0.995 0.990 0.627 0.464 36 36 PRO A 37 0.997 0.990 0.937 0.849 37 37 ASP A 38 0.964 0.931 0.195 0.211 38 38 TYR A 39 0.955 0.996 0.993 0.417 39 39 VAL A 40 0.999 0.999 0.999 40 40 GLY A 41 0.999 0.998 41 41 THR A 42 0.999 0.998 0.998 42 42 TYR A 43 0.999 0.999 0.999 0.797 43 43 TYR A 44 1.000 0.996 0.998 0.993 44 44 HIS A 45 0.998 0.999 0.999 0.991 45 45 LEU A 46 0.999 0.999 1.000 0.999 46 46 GLY A 47 1.000 0.998 47 47 LYS A 48 0.999 0.999 0.994 0.998 0.595 0.469 48 48 LEU A 49 0.999 0.999 0.998 1.000 49 49 TYR A 50 0.999 0.998 0.998 0.999 50 50 GLU A 51 0.999 0.997 0.998 0.994 0.550 51 51 ARG A 52 0.995 0.998 0.997 0.994 0.510 0.868 0.998 52 52 LEU A 53 0.999 0.998 0.998 0.999 53 53 ASP A 54 0.998 0.992 0.649 0.624 54 54 ARG A 55 0.992 0.993 0.999 0.996 0.998 0.904 0.998 55 55 THR A 56 0.999 0.998 0.997 56 56 ASP A 57 0.998 0.999 0.521 0.527 57 57 ASP A 58 0.999 0.998 0.995 0.803 58 58 ALA A 59 1.000 0.998 59 59 ILE A 60 0.999 0.999 0.998 0.999 60 60 ASP A 61 0.998 0.997 0.996 0.508 61 61 THR A 62 0.999 0.997 0.998 62 62 TYR A 63 0.999 0.999 0.998 0.999 63 63 ALA A 64 0.999 0.998 64 64 GLN A 65 0.998 0.999 0.856 0.991 0.950 65 65 GLY A 66 1.000 0.998 66 66 ILE A 67 0.999 0.999 0.999 0.999 67 67 GLU A 68 1.000 0.999 0.999 0.861 0.698 68 68 VAL A 69 1.000 1.000 0.999 69 69 ALA A 70 1.000 0.999 70 70 ARG A 71 0.998 0.996 0.998 0.994 0.499 0.715 0.998 71 71 GLU A 72 1.000 1.000 0.997 0.471 0.262 72 72 GLU A 73 0.996 0.996 0.996 0.998 0.781 73 73 GLY A 74 0.996 0.994 74 74 THR A 75 0.987 0.998 0.999 75 75 GLN A 76 0.998 0.998 0.995 0.544 0.485 76 76 LYS A 77 0.998 0.999 0.947 0.944 0.636 0.414 77 77 ASP A 78 0.998 0.999 0.996 0.539 78 78 LEU A 79 1.000 0.999 0.999 0.999 79 79 SER A 80 0.999 0.998 0.560 80 80 GLU A 81 0.998 0.997 0.996 0.662 0.638 81 81 LEU A 82 0.999 0.998 0.998 0.993 82 82 GLN A 83 0.999 0.998 0.999 0.999 0.978 83 83 ASP A 84 0.998 0.998 0.945 0.795 84 84 ALA A 85 0.999 0.998 85 85 LYS A 86 1.000 0.999 0.998 0.995 0.999 0.808 86 86 LEU A 87 0.999 0.999 0.996 0.999 87 87 LYS A 88 0.999 0.999 0.996 0.756 0.855 0.258 88 88 ALA A 89 0.997 0.997 89 89 GLU A 90 0.994 0.996 0.998 0.578 0.291 90 90 GLY A 91 0.980 0.965 91 91 LEU A 92 0.975 0.972 0.996 0.999 92 92 GLU A 93 0.859 0.567 0.589 0.509 0.253 HIS A 94 0.581 0.518 0.661 0.278 HIS A 95 0.601 0.681 0.231 0.256 HIS A 96 0.886 0.622 0.150 0.270 HIS A 97 0.539 0.461 0.273 0.337 HIS A 98 0.577 0.375 0.369 0.177 HIS A 99 0.713 0.438 0.228 Ranges: 1 from: A 3 to A 92 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[3..92],for model 1 is: 0.324 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 2 is: 0.385 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 3 is: 0.396 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 4 is: 0.443 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 5 is: 0.397 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 6 is: 0.479 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 7 is: 0.279 (*) > Kabsch RMSD of backbone atoms in res. A[3..92],for model 8 is: 0.413 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 9 is: 0.429 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 10 is: 0.434 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 11 is: 0.402 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 12 is: 0.340 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 13 is: 0.339 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 14 is: 0.361 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 15 is: 0.396 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 16 is: 0.520 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 17 is: 0.375 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 18 is: 0.358 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 19 is: 0.443 > Kabsch RMSD of backbone atoms in res. A[3..92],for model 20 is: 0.357 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..92], is: 0.393 > Range of RMSD values to reference struct. is 0.279 to 0.520 > 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[3..92],for model 1 is: 0.675 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 2 is: 0.705 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 3 is: 0.696 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 4 is: 0.760 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 5 is: 0.731 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 6 is: 0.776 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 7 is: 0.671 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 8 is: 0.686 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 9 is: 0.700 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 10 is: 0.762 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 11 is: 0.725 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 12 is: 0.714 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 13 is: 0.663 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 14 is: 0.649 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 15 is: 0.713 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 16 is: 0.802 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 17 is: 0.687 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 18 is: 0.734 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 19 is: 0.762 > Kabsch RMSD of heavy atoms in res. A[3..92],for model 20 is: 0.648 (*) > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[3..92], is: 0.713 > Range of RMSD values to reference struct. is 0.648 to 0.802 PdbStat> PdbStat> *END* of program detected, BYE! ...