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 `SPR104_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 82 MET LYS LYS MET ALA GLU PHE THR PHE GLU ILE GLU GLU > ReadCoordsPdb(): Counting models in file `SPR104_R3Cons_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 SPR104_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 52640 ATOM records read from file > ReadCoordsPdb(): --> 52640 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 `SPR104_R3Cons_em_bcr3.hbond' opened for reading 0 SANI-RDC constraints read 112 NOE-distance constraints (0 Ambiguous NOE/s) read 112 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 : 112 LONG RANGE H-BOND RESTR. (I-J)>=5 : 64 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 112 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 LYS A 3 0 0.0 0.0 0.0 0.0 0.0 MET A 4 0 0.0 0.0 0.0 0.0 0.0 ALA A 5 0 0.0 0.0 0.0 0.0 0.0 GLU A 6 0 0.0 0.0 0.0 0.0 0.0 PHE A 7 0 0.0 0.0 0.0 0.0 0.0 THR A 8 0 0.0 0.0 0.0 0.0 0.0 PHE 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 ILE A 11 0 0.0 0.0 0.0 0.0 0.0 GLU 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 HIS A 14 0 0.0 0.0 0.0 0.0 0.0 LEU A 15 0 0.0 0.0 0.0 0.0 0.0 LEU A 16 0 0.0 0.0 0.0 0.0 0.0 THR A 17 0 0.0 0.0 0.0 0.0 0.0 LEU A 18 0 0.0 0.0 0.0 0.0 0.0 SER A 19 0 0.0 0.0 0.0 0.0 0.0 GLU A 20 0 0.0 0.0 0.0 0.0 0.0 ASN A 21 0 0.0 0.0 0.0 0.0 0.0 GLU A 22 0 0.0 0.0 0.0 0.0 0.0 LYS A 23 0 0.0 0.0 0.0 0.0 0.0 GLY A 24 0 0.0 0.0 0.0 0.0 0.0 TRP A 25 0 0.0 0.0 0.0 0.0 0.0 THR A 26 0 0.0 0.0 0.0 0.0 0.0 LYS A 27 0 0.0 0.0 0.0 0.0 0.0 GLU A 28 0 0.0 0.0 0.0 0.0 0.0 ILE A 29 0 0.0 0.0 0.0 0.0 0.0 ASN A 30 0 0.0 0.0 0.0 0.0 0.0 ARG A 31 0 0.0 0.0 0.0 0.0 0.0 VAL A 32 0 0.0 0.0 0.0 0.0 0.0 SER A 33 0 0.0 0.0 0.0 0.0 0.0 PHE A 34 0 0.0 0.0 0.0 0.0 0.0 ASN A 35 0 0.0 0.0 0.0 0.0 0.0 GLY A 36 0 0.0 0.0 0.0 0.0 0.0 ALA A 37 0 0.0 0.0 0.0 0.0 0.0 PRO A 38 0 0.0 0.0 0.0 0.0 0.0 ALA A 39 0 0.0 0.0 0.0 0.0 0.0 LYS 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 ASP A 42 0 0.0 0.0 0.0 0.0 0.0 ILE A 43 0 0.0 0.0 0.0 0.0 0.0 ARG 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 TRP A 46 0 0.0 0.0 0.0 0.0 0.0 SER A 47 0 0.0 0.0 0.0 0.0 0.0 PRO A 48 0 0.0 0.0 0.0 0.0 0.0 ASP A 49 0 0.0 0.0 0.0 0.0 0.0 HIS A 50 0 0.0 0.0 0.0 0.0 0.0 THR 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 MET A 53 0 0.0 0.0 0.0 0.0 0.0 GLY A 54 0 0.0 0.0 0.0 0.0 0.0 LYS A 55 0 0.0 0.0 0.0 0.0 0.0 GLY A 56 0 0.0 0.0 0.0 0.0 0.0 ILE A 57 0 0.0 0.0 0.0 0.0 0.0 THR 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 SER A 60 0 0.0 0.0 0.0 0.0 0.0 ASN A 61 0 0.0 0.0 0.0 0.0 0.0 GLU A 62 0 0.0 0.0 0.0 0.0 0.0 GLU A 63 0 0.0 0.0 0.0 0.0 0.0 PHE A 64 0 0.0 0.0 0.0 0.0 0.0 GLN A 65 0 0.0 0.0 0.0 0.0 0.0 THR A 66 0 0.0 0.0 0.0 0.0 0.0 MET 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 ASP 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 PHE A 71 0 0.0 0.0 0.0 0.0 0.0 LYS A 72 0 0.0 0.0 0.0 0.0 0.0 GLY A 73 0 0.0 0.0 0.0 0.0 0.0 ASN 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 GLU A 76 0 0.0 0.0 0.0 0.0 0.0 HIS A 77 0 0.0 0.0 0.0 0.0 0.0 HIS A 78 0 0.0 0.0 0.0 0.0 0.0 HIS A 79 0 0.0 0.0 0.0 0.0 0.0 HIS A 80 0 0.0 0.0 0.0 0.0 0.0 HIS A 81 0 0.0 0.0 0.0 0.0 0.0 HIS A 82 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 LYS B 2 0 0.0 0.0 0.0 0.0 0.0 LYS B 3 0 0.0 0.0 0.0 0.0 0.0 MET B 4 0 0.0 0.0 0.0 0.0 0.0 ALA B 5 0 0.0 0.0 0.0 0.0 0.0 GLU B 6 0 0.0 0.0 0.0 0.0 0.0 PHE B 7 0 0.0 0.0 0.0 0.0 0.0 THR B 8 0 0.0 0.0 0.0 0.0 0.0 PHE 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 ILE B 11 0 0.0 0.0 0.0 0.0 0.0 GLU 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 HIS B 14 0 0.0 0.0 0.0 0.0 0.0 LEU B 15 0 0.0 0.0 0.0 0.0 0.0 LEU B 16 0 0.0 0.0 0.0 0.0 0.0 THR B 17 0 0.0 0.0 0.0 0.0 0.0 LEU B 18 0 0.0 0.0 0.0 0.0 0.0 SER B 19 0 0.0 0.0 0.0 0.0 0.0 GLU B 20 0 0.0 0.0 0.0 0.0 0.0 ASN B 21 0 0.0 0.0 0.0 0.0 0.0 GLU B 22 0 0.0 0.0 0.0 0.0 0.0 LYS B 23 0 0.0 0.0 0.0 0.0 0.0 GLY B 24 0 0.0 0.0 0.0 0.0 0.0 TRP B 25 0 0.0 0.0 0.0 0.0 0.0 THR B 26 0 0.0 0.0 0.0 0.0 0.0 LYS B 27 0 0.0 0.0 0.0 0.0 0.0 GLU B 28 0 0.0 0.0 0.0 0.0 0.0 ILE B 29 0 0.0 0.0 0.0 0.0 0.0 ASN B 30 0 0.0 0.0 0.0 0.0 0.0 ARG B 31 0 0.0 0.0 0.0 0.0 0.0 VAL B 32 0 0.0 0.0 0.0 0.0 0.0 SER B 33 0 0.0 0.0 0.0 0.0 0.0 PHE B 34 0 0.0 0.0 0.0 0.0 0.0 ASN B 35 0 0.0 0.0 0.0 0.0 0.0 GLY B 36 0 0.0 0.0 0.0 0.0 0.0 ALA B 37 0 0.0 0.0 0.0 0.0 0.0 PRO B 38 0 0.0 0.0 0.0 0.0 0.0 ALA B 39 0 0.0 0.0 0.0 0.0 0.0 LYS B 40 0 0.0 0.0 0.0 0.0 0.0 PHE B 41 0 0.0 0.0 0.0 0.0 0.0 ASP B 42 0 0.0 0.0 0.0 0.0 0.0 ILE B 43 0 0.0 0.0 0.0 0.0 0.0 ARG 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 TRP B 46 0 0.0 0.0 0.0 0.0 0.0 SER B 47 0 0.0 0.0 0.0 0.0 0.0 PRO B 48 0 0.0 0.0 0.0 0.0 0.0 ASP B 49 0 0.0 0.0 0.0 0.0 0.0 HIS B 50 0 0.0 0.0 0.0 0.0 0.0 THR 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 MET B 53 0 0.0 0.0 0.0 0.0 0.0 GLY B 54 0 0.0 0.0 0.0 0.0 0.0 LYS B 55 0 0.0 0.0 0.0 0.0 0.0 GLY B 56 0 0.0 0.0 0.0 0.0 0.0 ILE B 57 0 0.0 0.0 0.0 0.0 0.0 THR 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 SER B 60 0 0.0 0.0 0.0 0.0 0.0 ASN B 61 0 0.0 0.0 0.0 0.0 0.0 GLU B 62 0 0.0 0.0 0.0 0.0 0.0 GLU B 63 0 0.0 0.0 0.0 0.0 0.0 PHE B 64 0 0.0 0.0 0.0 0.0 0.0 GLN B 65 0 0.0 0.0 0.0 0.0 0.0 THR B 66 0 0.0 0.0 0.0 0.0 0.0 MET 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 ASP 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 PHE B 71 0 0.0 0.0 0.0 0.0 0.0 LYS B 72 0 0.0 0.0 0.0 0.0 0.0 GLY B 73 0 0.0 0.0 0.0 0.0 0.0 ASN B 74 0 0.0 0.0 0.0 0.0 0.0 LEU B 75 0 0.0 0.0 0.0 0.0 0.0 GLU B 76 0 0.0 0.0 0.0 0.0 0.0 HIS B 77 0 0.0 0.0 0.0 0.0 0.0 HIS B 78 0 0.0 0.0 0.0 0.0 0.0 HIS B 79 0 0.0 0.0 0.0 0.0 0.0 HIS B 80 0 0.0 0.0 0.0 0.0 0.0 HIS B 81 0 0.0 0.0 0.0 0.0 0.0 HIS B 82 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] ?_