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 `CSR4_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR 2JR2_R3EM.PDB, 20 MODEL/S 2JR2_R3EM.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 76 MET PRO ILE VAL SER LYS TYR SER ASN GLU ARG VAL GLU > ReadCoordsPdb(): Counting models in file `CSR4_R3_em_bcr3.pdb'; Model: > 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 CSR4_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 48960 ATOM records read from file > ReadCoordsPdb(): --> 48960 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 `CSR4_R3_em_bcr3.hbond' opened for reading 0 SANI-RDC constraints read 124 NOE-distance constraints (0 Ambiguous NOE/s) read 124 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 : 124 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 124 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 PRO A 2 0 0.0 0.0 0.0 0.0 0.0 ILE A 3 0 0.0 0.0 0.0 0.0 0.0 VAL 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 LYS A 6 0 0.0 0.0 0.0 0.0 0.0 TYR A 7 0 0.0 0.0 0.0 0.0 0.0 SER A 8 0 0.0 0.0 0.0 0.0 0.0 ASN A 9 0 0.0 0.0 0.0 0.0 0.0 GLU A 10 0 0.0 0.0 0.0 0.0 0.0 ARG A 11 0 0.0 0.0 0.0 0.0 0.0 VAL A 12 0 0.0 0.0 0.0 0.0 0.0 GLU A 13 0 0.0 0.0 0.0 0.0 0.0 LYS A 14 0 0.0 0.0 0.0 0.0 0.0 ILE A 15 0 0.0 0.0 0.0 0.0 0.0 ILE A 16 0 0.0 0.0 0.0 0.0 0.0 GLN A 17 0 0.0 0.0 0.0 0.0 0.0 ASP A 18 0 0.0 0.0 0.0 0.0 0.0 LEU A 19 0 0.0 0.0 0.0 0.0 0.0 LEU A 20 0 0.0 0.0 0.0 0.0 0.0 ASP A 21 0 0.0 0.0 0.0 0.0 0.0 VAL A 22 0 0.0 0.0 0.0 0.0 0.0 LEU A 23 0 0.0 0.0 0.0 0.0 0.0 VAL A 24 0 0.0 0.0 0.0 0.0 0.0 LYS A 25 0 0.0 0.0 0.0 0.0 0.0 GLU A 26 0 0.0 0.0 0.0 0.0 0.0 GLU A 27 0 0.0 0.0 0.0 0.0 0.0 VAL A 28 0 0.0 0.0 0.0 0.0 0.0 THR A 29 0 0.0 0.0 0.0 0.0 0.0 PRO A 30 0 0.0 0.0 0.0 0.0 0.0 ASP A 31 0 0.0 0.0 0.0 0.0 0.0 LEU A 32 0 0.0 0.0 0.0 0.0 0.0 ALA 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 MET A 35 0 0.0 0.0 0.0 0.0 0.0 CYS A 36 0 0.0 0.0 0.0 0.0 0.0 LEU A 37 0 0.0 0.0 0.0 0.0 0.0 GLY A 38 0 0.0 0.0 0.0 0.0 0.0 ASN 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 THR A 42 0 0.0 0.0 0.0 0.0 0.0 ASN 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 ILE A 45 0 0.0 0.0 0.0 0.0 0.0 ALA A 46 0 0.0 0.0 0.0 0.0 0.0 GLN A 47 0 0.0 0.0 0.0 0.0 0.0 VAL A 48 0 0.0 0.0 0.0 0.0 0.0 PRO A 49 0 0.0 0.0 0.0 0.0 0.0 GLU A 50 0 0.0 0.0 0.0 0.0 0.0 SER A 51 0 0.0 0.0 0.0 0.0 0.0 LYS A 52 0 0.0 0.0 0.0 0.0 0.0 ARG A 53 0 0.0 0.0 0.0 0.0 0.0 VAL 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 VAL A 56 0 0.0 0.0 0.0 0.0 0.0 VAL A 57 0 0.0 0.0 0.0 0.0 0.0 ASP A 58 0 0.0 0.0 0.0 0.0 0.0 ASN A 59 0 0.0 0.0 0.0 0.0 0.0 PHE A 60 0 0.0 0.0 0.0 0.0 0.0 THR A 61 0 0.0 0.0 0.0 0.0 0.0 LYS A 62 0 0.0 0.0 0.0 0.0 0.0 ALA A 63 0 0.0 0.0 0.0 0.0 0.0 LEU A 64 0 0.0 0.0 0.0 0.0 0.0 LYS A 65 0 0.0 0.0 0.0 0.0 0.0 GLN A 66 0 0.0 0.0 0.0 0.0 0.0 SER 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 LEU A 69 0 0.0 0.0 0.0 0.0 0.0 GLU A 70 0 0.0 0.0 0.0 0.0 0.0 HIS A 71 0 0.0 0.0 0.0 0.0 0.0 HIS A 72 0 0.0 0.0 0.0 0.0 0.0 HIS A 73 0 0.0 0.0 0.0 0.0 0.0 HIS A 74 0 0.0 0.0 0.0 0.0 0.0 HIS A 75 0 0.0 0.0 0.0 0.0 0.0 HIS A 76 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 PRO B 2 0 0.0 0.0 0.0 0.0 0.0 ILE B 3 0 0.0 0.0 0.0 0.0 0.0 VAL 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 LYS B 6 0 0.0 0.0 0.0 0.0 0.0 TYR B 7 0 0.0 0.0 0.0 0.0 0.0 SER B 8 0 0.0 0.0 0.0 0.0 0.0 ASN B 9 0 0.0 0.0 0.0 0.0 0.0 GLU B 10 0 0.0 0.0 0.0 0.0 0.0 ARG B 11 0 0.0 0.0 0.0 0.0 0.0 VAL B 12 0 0.0 0.0 0.0 0.0 0.0 GLU B 13 0 0.0 0.0 0.0 0.0 0.0 LYS B 14 0 0.0 0.0 0.0 0.0 0.0 ILE B 15 0 0.0 0.0 0.0 0.0 0.0 ILE B 16 0 0.0 0.0 0.0 0.0 0.0 GLN B 17 0 0.0 0.0 0.0 0.0 0.0 ASP B 18 0 0.0 0.0 0.0 0.0 0.0 LEU B 19 0 0.0 0.0 0.0 0.0 0.0 LEU B 20 0 0.0 0.0 0.0 0.0 0.0 ASP B 21 0 0.0 0.0 0.0 0.0 0.0 VAL B 22 0 0.0 0.0 0.0 0.0 0.0 LEU B 23 0 0.0 0.0 0.0 0.0 0.0 VAL B 24 0 0.0 0.0 0.0 0.0 0.0 LYS B 25 0 0.0 0.0 0.0 0.0 0.0 GLU B 26 0 0.0 0.0 0.0 0.0 0.0 GLU B 27 0 0.0 0.0 0.0 0.0 0.0 VAL B 28 0 0.0 0.0 0.0 0.0 0.0 THR B 29 0 0.0 0.0 0.0 0.0 0.0 PRO B 30 0 0.0 0.0 0.0 0.0 0.0 ASP B 31 0 0.0 0.0 0.0 0.0 0.0 LEU B 32 0 0.0 0.0 0.0 0.0 0.0 ALA 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 MET B 35 0 0.0 0.0 0.0 0.0 0.0 CYS B 36 0 0.0 0.0 0.0 0.0 0.0 LEU B 37 0 0.0 0.0 0.0 0.0 0.0 GLY B 38 0 0.0 0.0 0.0 0.0 0.0 ASN 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 THR B 42 0 0.0 0.0 0.0 0.0 0.0 ASN 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 ILE B 45 0 0.0 0.0 0.0 0.0 0.0 ALA B 46 0 0.0 0.0 0.0 0.0 0.0 GLN B 47 0 0.0 0.0 0.0 0.0 0.0 VAL B 48 0 0.0 0.0 0.0 0.0 0.0 PRO B 49 0 0.0 0.0 0.0 0.0 0.0 GLU B 50 0 0.0 0.0 0.0 0.0 0.0 SER B 51 0 0.0 0.0 0.0 0.0 0.0 LYS B 52 0 0.0 0.0 0.0 0.0 0.0 ARG B 53 0 0.0 0.0 0.0 0.0 0.0 VAL 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 VAL B 56 0 0.0 0.0 0.0 0.0 0.0 VAL B 57 0 0.0 0.0 0.0 0.0 0.0 ASP B 58 0 0.0 0.0 0.0 0.0 0.0 ASN B 59 0 0.0 0.0 0.0 0.0 0.0 PHE B 60 0 0.0 0.0 0.0 0.0 0.0 THR B 61 0 0.0 0.0 0.0 0.0 0.0 LYS B 62 0 0.0 0.0 0.0 0.0 0.0 ALA B 63 0 0.0 0.0 0.0 0.0 0.0 LEU B 64 0 0.0 0.0 0.0 0.0 0.0 LYS B 65 0 0.0 0.0 0.0 0.0 0.0 GLN B 66 0 0.0 0.0 0.0 0.0 0.0 SER 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 LEU B 69 0 0.0 0.0 0.0 0.0 0.0 GLU B 70 0 0.0 0.0 0.0 0.0 0.0 HIS B 71 0 0.0 0.0 0.0 0.0 0.0 HIS B 72 0 0.0 0.0 0.0 0.0 0.0 HIS B 73 0 0.0 0.0 0.0 0.0 0.0 HIS B 74 0 0.0 0.0 0.0 0.0 0.0 HIS B 75 0 0.0 0.0 0.0 0.0 0.0 HIS B 76 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] ?_