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 `ZR18_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 19-JUN-03 1PQX > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF STAPHYLOCOCCUS AUREUS PROTEIN > ReadCoordsPdb(): >> TITLE 2 SAV1430. NORTHEAST STRUCUTRAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 ZR18. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): Counting models in file `ZR18_NMR_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 10 model(s) > ReadCoordsPdb(): what model do you want [(1 to 10) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file ZR18_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (10) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 14440 ATOM records read from file > ReadCoordsPdb(): --> 14440 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> > locate_file(): file `ZR18_NMR_em_bcr3.hbond' opened for reading 0 SANI-RDC constraints read 54 NOE-distance constraints (0 Ambiguous NOE/s) read 54 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 : 54 LONG RANGE H-BOND RESTR. (I-J)>=5 : 32 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 54 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 LYS 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 ILE 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 ILE A 6 0 0.0 0.0 0.0 0.0 0.0 SER A 7 0 0.0 0.0 0.0 0.0 0.0 GLU A 8 0 0.0 0.0 0.0 0.0 0.0 THR A 9 0 0.0 0.0 0.0 0.0 0.0 PRO A 10 0 0.0 0.0 0.0 0.0 0.0 ASN A 11 0 0.0 0.0 0.0 0.0 0.0 HIS A 12 0 0.0 0.0 0.0 0.0 0.0 ASN A 13 0 0.0 0.0 0.0 0.0 0.0 THR A 14 0 0.0 0.0 0.0 0.0 0.0 MET A 15 0 0.0 0.0 0.0 0.0 0.0 LYS A 16 0 0.0 0.0 0.0 0.0 0.0 ILE A 17 0 0.0 0.0 0.0 0.0 0.0 THR 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 SER A 20 0 0.0 0.0 0.0 0.0 0.0 GLU A 21 0 0.0 0.0 0.0 0.0 0.0 SER A 22 0 0.0 0.0 0.0 0.0 0.0 ARG A 23 0 0.0 0.0 0.0 0.0 0.0 GLU 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 MET A 26 0 0.0 0.0 0.0 0.0 0.0 THR A 27 0 0.0 0.0 0.0 0.0 0.0 SER A 28 0 0.0 0.0 0.0 0.0 0.0 ASP A 29 0 0.0 0.0 0.0 0.0 0.0 THR A 30 0 0.0 0.0 0.0 0.0 0.0 TYR A 31 0 0.0 0.0 0.0 0.0 0.0 THR A 32 0 0.0 0.0 0.0 0.0 0.0 LYS A 33 0 0.0 0.0 0.0 0.0 0.0 VAL A 34 0 0.0 0.0 0.0 0.0 0.0 ASP A 35 0 0.0 0.0 0.0 0.0 0.0 ASP A 36 0 0.0 0.0 0.0 0.0 0.0 SER A 37 0 0.0 0.0 0.0 0.0 0.0 GLN A 38 0 0.0 0.0 0.0 0.0 0.0 PRO 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 PHE A 41 0 0.0 0.0 0.0 0.0 0.0 ILE 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 ASP 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 LEU A 46 0 0.0 0.0 0.0 0.0 0.0 LYS 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 GLU A 49 0 0.0 0.0 0.0 0.0 0.0 GLY A 50 0 0.0 0.0 0.0 0.0 0.0 VAL 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 SER A 53 0 0.0 0.0 0.0 0.0 0.0 ILE A 54 0 0.0 0.0 0.0 0.0 0.0 PHE A 55 0 0.0 0.0 0.0 0.0 0.0 HIS 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 MET A 58 0 0.0 0.0 0.0 0.0 0.0 ASP 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 ILE A 61 0 0.0 0.0 0.0 0.0 0.0 SER A 62 0 0.0 0.0 0.0 0.0 0.0 VAL A 63 0 0.0 0.0 0.0 0.0 0.0 ASP 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 GLU A 66 0 0.0 0.0 0.0 0.0 0.0 ASN A 67 0 0.0 0.0 0.0 0.0 0.0 ASP A 68 0 0.0 0.0 0.0 0.0 0.0 ALA A 69 0 0.0 0.0 0.0 0.0 0.0 ASN A 70 0 0.0 0.0 0.0 0.0 0.0 TRP A 71 0 0.0 0.0 0.0 0.0 0.0 GLU A 72 0 0.0 0.0 0.0 0.0 0.0 THR A 73 0 0.0 0.0 0.0 0.0 0.0 VAL A 74 0 0.0 0.0 0.0 0.0 0.0 LEU A 75 0 0.0 0.0 0.0 0.0 0.0 PRO A 76 0 0.0 0.0 0.0 0.0 0.0 LYS A 77 0 0.0 0.0 0.0 0.0 0.0 VAL A 78 0 0.0 0.0 0.0 0.0 0.0 GLU A 79 0 0.0 0.0 0.0 0.0 0.0 ALA A 80 0 0.0 0.0 0.0 0.0 0.0 VAL A 81 0 0.0 0.0 0.0 0.0 0.0 PHE A 82 0 0.0 0.0 0.0 0.0 0.0 GLU A 83 0 0.0 0.0 0.0 0.0 0.0 LEU A 84 0 0.0 0.0 0.0 0.0 0.0 GLU A 85 0 0.0 0.0 0.0 0.0 0.0 HIS A 86 0 0.0 0.0 0.0 0.0 0.0 HIS A 87 0 0.0 0.0 0.0 0.0 0.0 HIS A 88 0 0.0 0.0 0.0 0.0 0.0 HIS A 89 0 0.0 0.0 0.0 0.0 0.0 HIS A 90 0 0.0 0.0 0.0 0.0 0.0 HIS A 91 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] ?_