Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.9 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2013 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.9-exp mar may 14 00:20:00 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 ...) 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 `MBR242E_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 19 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 18 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 108 MET ALA GLY GLN SER ASP ARG LYS ALA ALA LEU LEU ASP > ReadCoordsPdb(): Counting models in file `MBR242E_R3Cons_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file MBR242E_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (18) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 59652 ATOM records read from file > ReadCoordsPdb(): --> 59652 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** x-mer, 2 [2] chains ** PdbStat> > locate_file(): file `MBR242E_R3Cons_em_bcr3.hbond' opened for reading 0 SANI-RDC constraints read 228 NOE-distance constraints (0 Ambiguous NOE/s) read 228 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 0 INTRA-RESIDUE RESTRAINTS (I=J) : 0 SEQUENTIAL RESTRAINTS (I-J)=1 : 0 BACKBONE-BACKBONE : 0 BACKBONE-SIDE CHAIN : 0 SIDE CHAIN-SIDE CHAIN : 0 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 0 BACKBONE-BACKBONE : 0 BACKBONE-SIDE CHAIN : 0 SIDE CHAIN-SIDE CHAIN : 0 LONG RANGE RESTRAINTS (I-J)>=5 : 0 TOTAL HYDROGEN BOND RESTRAINTS : 228 LONG RANGE H-BOND RESTR. (I-J)>=5 : 40 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 228 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 0 0.0 0.0 0.0 0.0 0.0 ALA A 2 0 0.0 0.0 0.0 0.0 0.0 GLY A 3 0 0.0 0.0 0.0 0.0 0.0 GLN A 4 0 0.0 0.0 0.0 0.0 0.0 SER A 5 0 0.0 0.0 0.0 0.0 0.0 ASP A 6 0 0.0 0.0 0.0 0.0 0.0 ARG A 7 0 0.0 0.0 0.0 0.0 0.0 LYS A 8 0 0.0 0.0 0.0 0.0 0.0 ALA A 9 0 0.0 0.0 0.0 0.0 0.0 ALA A 10 0 0.0 0.0 0.0 0.0 0.0 LEU A 11 0 0.0 0.0 0.0 0.0 0.0 LEU A 12 0 0.0 0.0 0.0 0.0 0.0 ASP A 13 0 0.0 0.0 0.0 0.0 0.0 GLN A 14 0 0.0 0.0 0.0 0.0 0.0 VAL A 15 0 0.0 0.0 0.0 0.0 0.0 ALA A 16 0 0.0 0.0 0.0 0.0 0.0 ARG A 17 0 0.0 0.0 0.0 0.0 0.0 VAL A 18 0 0.0 0.0 0.0 0.0 0.0 GLY A 19 0 0.0 0.0 0.0 0.0 0.0 LYS A 20 0 0.0 0.0 0.0 0.0 0.0 ALA A 21 0 0.0 0.0 0.0 0.0 0.0 LEU A 22 0 0.0 0.0 0.0 0.0 0.0 ALA A 23 0 0.0 0.0 0.0 0.0 0.0 ASN A 24 0 0.0 0.0 0.0 0.0 0.0 GLY A 25 0 0.0 0.0 0.0 0.0 0.0 ARG A 26 0 0.0 0.0 0.0 0.0 0.0 ARG A 27 0 0.0 0.0 0.0 0.0 0.0 LEU A 28 0 0.0 0.0 0.0 0.0 0.0 GLN A 29 0 0.0 0.0 0.0 0.0 0.0 ILE A 30 0 0.0 0.0 0.0 0.0 0.0 LEU A 31 0 0.0 0.0 0.0 0.0 0.0 ASP A 32 0 0.0 0.0 0.0 0.0 0.0 LEU A 33 0 0.0 0.0 0.0 0.0 0.0 LEU A 34 0 0.0 0.0 0.0 0.0 0.0 ALA A 35 0 0.0 0.0 0.0 0.0 0.0 GLN A 36 0 0.0 0.0 0.0 0.0 0.0 GLY A 37 0 0.0 0.0 0.0 0.0 0.0 GLU A 38 0 0.0 0.0 0.0 0.0 0.0 ARG A 39 0 0.0 0.0 0.0 0.0 0.0 ALA A 40 0 0.0 0.0 0.0 0.0 0.0 VAL A 41 0 0.0 0.0 0.0 0.0 0.0 GLU A 42 0 0.0 0.0 0.0 0.0 0.0 ALA A 43 0 0.0 0.0 0.0 0.0 0.0 ILE A 44 0 0.0 0.0 0.0 0.0 0.0 ALA A 45 0 0.0 0.0 0.0 0.0 0.0 THR A 46 0 0.0 0.0 0.0 0.0 0.0 ALA A 47 0 0.0 0.0 0.0 0.0 0.0 THR A 48 0 0.0 0.0 0.0 0.0 0.0 GLY A 49 0 0.0 0.0 0.0 0.0 0.0 MET A 50 0 0.0 0.0 0.0 0.0 0.0 ASN A 51 0 0.0 0.0 0.0 0.0 0.0 LEU A 52 0 0.0 0.0 0.0 0.0 0.0 THR A 53 0 0.0 0.0 0.0 0.0 0.0 THR A 54 0 0.0 0.0 0.0 0.0 0.0 ALA A 55 0 0.0 0.0 0.0 0.0 0.0 SER A 56 0 0.0 0.0 0.0 0.0 0.0 ALA A 57 0 0.0 0.0 0.0 0.0 0.0 ASN A 58 0 0.0 0.0 0.0 0.0 0.0 LEU A 59 0 0.0 0.0 0.0 0.0 0.0 GLN A 60 0 0.0 0.0 0.0 0.0 0.0 ALA A 61 0 0.0 0.0 0.0 0.0 0.0 LEU A 62 0 0.0 0.0 0.0 0.0 0.0 LYS A 63 0 0.0 0.0 0.0 0.0 0.0 SER A 64 0 0.0 0.0 0.0 0.0 0.0 GLY A 65 0 0.0 0.0 0.0 0.0 0.0 GLY A 66 0 0.0 0.0 0.0 0.0 0.0 LEU A 67 0 0.0 0.0 0.0 0.0 0.0 VAL A 68 0 0.0 0.0 0.0 0.0 0.0 GLU A 69 0 0.0 0.0 0.0 0.0 0.0 ALA A 70 0 0.0 0.0 0.0 0.0 0.0 ARG A 71 0 0.0 0.0 0.0 0.0 0.0 ARG A 72 0 0.0 0.0 0.0 0.0 0.0 GLU A 73 0 0.0 0.0 0.0 0.0 0.0 GLY A 74 0 0.0 0.0 0.0 0.0 0.0 THR A 75 0 0.0 0.0 0.0 0.0 0.0 ARG A 76 0 0.0 0.0 0.0 0.0 0.0 GLN A 77 0 0.0 0.0 0.0 0.0 0.0 TYR A 78 0 0.0 0.0 0.0 0.0 0.0 TYR A 79 0 0.0 0.0 0.0 0.0 0.0 ARG A 80 0 0.0 0.0 0.0 0.0 0.0 ILE A 81 0 0.0 0.0 0.0 0.0 0.0 ALA A 82 0 0.0 0.0 0.0 0.0 0.0 GLY A 83 0 0.0 0.0 0.0 0.0 0.0 GLU A 84 0 0.0 0.0 0.0 0.0 0.0 ASP A 85 0 0.0 0.0 0.0 0.0 0.0 VAL A 86 0 0.0 0.0 0.0 0.0 0.0 ALA A 87 0 0.0 0.0 0.0 0.0 0.0 ARG A 88 0 0.0 0.0 0.0 0.0 0.0 LEU A 89 0 0.0 0.0 0.0 0.0 0.0 PHE A 90 0 0.0 0.0 0.0 0.0 0.0 ALA A 91 0 0.0 0.0 0.0 0.0 0.0 LEU A 92 0 0.0 0.0 0.0 0.0 0.0 VAL A 93 0 0.0 0.0 0.0 0.0 0.0 GLN A 94 0 0.0 0.0 0.0 0.0 0.0 VAL A 95 0 0.0 0.0 0.0 0.0 0.0 VAL A 96 0 0.0 0.0 0.0 0.0 0.0 ALA A 97 0 0.0 0.0 0.0 0.0 0.0 ASP A 98 0 0.0 0.0 0.0 0.0 0.0 GLU A 99 0 0.0 0.0 0.0 0.0 0.0 HIS A 100 0 0.0 0.0 0.0 0.0 0.0 LEU A 101 0 0.0 0.0 0.0 0.0 0.0 GLU A 102 0 0.0 0.0 0.0 0.0 0.0 HIS A 103 0 0.0 0.0 0.0 0.0 0.0 HIS A 104 0 0.0 0.0 0.0 0.0 0.0 HIS A 105 0 0.0 0.0 0.0 0.0 0.0 HIS A 106 0 0.0 0.0 0.0 0.0 0.0 HIS A 107 0 0.0 0.0 0.0 0.0 0.0 HIS A 108 0 0.0 0.0 0.0 0.0 0.0 MET B 1 0 0.0 0.0 0.0 0.0 0.0 ALA B 2 0 0.0 0.0 0.0 0.0 0.0 GLY B 3 0 0.0 0.0 0.0 0.0 0.0 GLN B 4 0 0.0 0.0 0.0 0.0 0.0 SER B 5 0 0.0 0.0 0.0 0.0 0.0 ASP B 6 0 0.0 0.0 0.0 0.0 0.0 ARG B 7 0 0.0 0.0 0.0 0.0 0.0 LYS B 8 0 0.0 0.0 0.0 0.0 0.0 ALA B 9 0 0.0 0.0 0.0 0.0 0.0 ALA B 10 0 0.0 0.0 0.0 0.0 0.0 LEU B 11 0 0.0 0.0 0.0 0.0 0.0 LEU B 12 0 0.0 0.0 0.0 0.0 0.0 ASP B 13 0 0.0 0.0 0.0 0.0 0.0 GLN B 14 0 0.0 0.0 0.0 0.0 0.0 VAL B 15 0 0.0 0.0 0.0 0.0 0.0 ALA B 16 0 0.0 0.0 0.0 0.0 0.0 ARG B 17 0 0.0 0.0 0.0 0.0 0.0 VAL B 18 0 0.0 0.0 0.0 0.0 0.0 GLY B 19 0 0.0 0.0 0.0 0.0 0.0 LYS B 20 0 0.0 0.0 0.0 0.0 0.0 ALA B 21 0 0.0 0.0 0.0 0.0 0.0 LEU B 22 0 0.0 0.0 0.0 0.0 0.0 ALA B 23 0 0.0 0.0 0.0 0.0 0.0 ASN B 24 0 0.0 0.0 0.0 0.0 0.0 GLY B 25 0 0.0 0.0 0.0 0.0 0.0 ARG B 26 0 0.0 0.0 0.0 0.0 0.0 ARG B 27 0 0.0 0.0 0.0 0.0 0.0 LEU B 28 0 0.0 0.0 0.0 0.0 0.0 GLN B 29 0 0.0 0.0 0.0 0.0 0.0 ILE B 30 0 0.0 0.0 0.0 0.0 0.0 LEU B 31 0 0.0 0.0 0.0 0.0 0.0 ASP B 32 0 0.0 0.0 0.0 0.0 0.0 LEU B 33 0 0.0 0.0 0.0 0.0 0.0 LEU B 34 0 0.0 0.0 0.0 0.0 0.0 ALA B 35 0 0.0 0.0 0.0 0.0 0.0 GLN B 36 0 0.0 0.0 0.0 0.0 0.0 GLY B 37 0 0.0 0.0 0.0 0.0 0.0 GLU B 38 0 0.0 0.0 0.0 0.0 0.0 ARG B 39 0 0.0 0.0 0.0 0.0 0.0 ALA B 40 0 0.0 0.0 0.0 0.0 0.0 VAL B 41 0 0.0 0.0 0.0 0.0 0.0 GLU B 42 0 0.0 0.0 0.0 0.0 0.0 ALA B 43 0 0.0 0.0 0.0 0.0 0.0 ILE B 44 0 0.0 0.0 0.0 0.0 0.0 ALA B 45 0 0.0 0.0 0.0 0.0 0.0 THR B 46 0 0.0 0.0 0.0 0.0 0.0 ALA B 47 0 0.0 0.0 0.0 0.0 0.0 THR B 48 0 0.0 0.0 0.0 0.0 0.0 GLY B 49 0 0.0 0.0 0.0 0.0 0.0 MET B 50 0 0.0 0.0 0.0 0.0 0.0 ASN B 51 0 0.0 0.0 0.0 0.0 0.0 LEU B 52 0 0.0 0.0 0.0 0.0 0.0 THR B 53 0 0.0 0.0 0.0 0.0 0.0 THR B 54 0 0.0 0.0 0.0 0.0 0.0 ALA B 55 0 0.0 0.0 0.0 0.0 0.0 SER B 56 0 0.0 0.0 0.0 0.0 0.0 ALA B 57 0 0.0 0.0 0.0 0.0 0.0 ASN B 58 0 0.0 0.0 0.0 0.0 0.0 LEU B 59 0 0.0 0.0 0.0 0.0 0.0 GLN B 60 0 0.0 0.0 0.0 0.0 0.0 ALA B 61 0 0.0 0.0 0.0 0.0 0.0 LEU B 62 0 0.0 0.0 0.0 0.0 0.0 LYS B 63 0 0.0 0.0 0.0 0.0 0.0 SER B 64 0 0.0 0.0 0.0 0.0 0.0 GLY B 65 0 0.0 0.0 0.0 0.0 0.0 GLY B 66 0 0.0 0.0 0.0 0.0 0.0 LEU B 67 0 0.0 0.0 0.0 0.0 0.0 VAL B 68 0 0.0 0.0 0.0 0.0 0.0 GLU B 69 0 0.0 0.0 0.0 0.0 0.0 ALA B 70 0 0.0 0.0 0.0 0.0 0.0 ARG B 71 0 0.0 0.0 0.0 0.0 0.0 ARG B 72 0 0.0 0.0 0.0 0.0 0.0 GLU B 73 0 0.0 0.0 0.0 0.0 0.0 GLY B 74 0 0.0 0.0 0.0 0.0 0.0 THR B 75 0 0.0 0.0 0.0 0.0 0.0 ARG B 76 0 0.0 0.0 0.0 0.0 0.0 GLN B 77 0 0.0 0.0 0.0 0.0 0.0 TYR B 78 0 0.0 0.0 0.0 0.0 0.0 TYR B 79 0 0.0 0.0 0.0 0.0 0.0 ARG B 80 0 0.0 0.0 0.0 0.0 0.0 ILE B 81 0 0.0 0.0 0.0 0.0 0.0 ALA B 82 0 0.0 0.0 0.0 0.0 0.0 GLY B 83 0 0.0 0.0 0.0 0.0 0.0 GLU B 84 0 0.0 0.0 0.0 0.0 0.0 ASP B 85 0 0.0 0.0 0.0 0.0 0.0 VAL B 86 0 0.0 0.0 0.0 0.0 0.0 ALA B 87 0 0.0 0.0 0.0 0.0 0.0 ARG B 88 0 0.0 0.0 0.0 0.0 0.0 LEU B 89 0 0.0 0.0 0.0 0.0 0.0 PHE B 90 0 0.0 0.0 0.0 0.0 0.0 ALA B 91 0 0.0 0.0 0.0 0.0 0.0 LEU B 92 0 0.0 0.0 0.0 0.0 0.0 VAL B 93 0 0.0 0.0 0.0 0.0 0.0 GLN B 94 0 0.0 0.0 0.0 0.0 0.0 VAL B 95 0 0.0 0.0 0.0 0.0 0.0 VAL B 96 0 0.0 0.0 0.0 0.0 0.0 ALA B 97 0 0.0 0.0 0.0 0.0 0.0 ASP B 98 0 0.0 0.0 0.0 0.0 0.0 GLU B 99 0 0.0 0.0 0.0 0.0 0.0 HIS B 100 0 0.0 0.0 0.0 0.0 0.0 LEU B 101 0 0.0 0.0 0.0 0.0 0.0 GLU B 102 0 0.0 0.0 0.0 0.0 0.0 HIS B 103 0 0.0 0.0 0.0 0.0 0.0 HIS B 104 0 0.0 0.0 0.0 0.0 0.0 HIS B 105 0 0.0 0.0 0.0 0.0 0.0 HIS B 106 0 0.0 0.0 0.0 0.0 0.0 HIS B 107 0 0.0 0.0 0.0 0.0 0.0 HIS B 108 0 0.0 0.0 0.0 0.0 0.0 TOTAL 0 0.0 0.0 0.0 0.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_