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 `STR70_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 142 MET ALA ASN ASP THR PRO PHE SER ALA LEU TRP GLN ARG 1 > ReadCoordsPdb(): Counting models in file `STR70_R3_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(): I'm reading file STR70_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2249 ATOM records read from file > ReadCoordsPdb(): --> 2249 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2249 (721 C, 1109 H, 210 O, 206 N, 3 S, 0 Q, 0 Metals) > INFO_mol: # residues: 142 (Avg. mol. weight: 113.5) > INFO_mol: # -- M.W. : 16118.9 g/mol. (16.12 kD) Estimated RoG : 14.46 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `STR70_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 142 > INFO_mol: Radius of Gyration : 14.7722 angstroms > INFO_mol: Center of Masses: x_cm(0.044), y_cm(4.329), z_cm(1.242) > INFO_res: MANDTPFSAL WQRLLTRGWQ PVEASTVDDW IKRVGDGVIL LSSDPRRTPE > INFO_res: VSDNPVMIAE LLREFPQFDW QVAVADLEQS EAIGDRFNVR RFPATLVFTD > INFO_res: GKLRGALSGI HPWAELLTLM RSIVDTPAAQ ETVQLEHHHH HH > INFO_res: > INFO_res: MET ALA ASN ASP THR PRO PHE SER ALA LEU TRP GLN > INFO_res: ARG LEU LEU THR ARG GLY TRP GLN PRO VAL GLU ALA > INFO_res: SER THR VAL ASP ASP TRP ILE LYS ARG VAL GLY ASP > INFO_res: GLY VAL ILE LEU LEU SER SER ASP PRO ARG ARG THR > INFO_res: PRO GLU VAL SER ASP ASN PRO VAL MET ILE ALA GLU > INFO_res: LEU LEU ARG GLU PHE PRO GLN PHE ASP TRP GLN VAL > INFO_res: ALA VAL ALA ASP LEU GLU GLN SER GLU ALA ILE GLY > INFO_res: ASP ARG PHE ASN VAL ARG ARG PHE PRO ALA THR LEU > INFO_res: VAL PHE THR ASP GLY LYS LEU ARG GLY ALA LEU SER > INFO_res: GLY ILE HIS PRO TRP ALA GLU LEU LEU THR LEU MET > INFO_res: ARG SER ILE VAL ASP THR PRO ALA ALA GLN GLU THR > INFO_res: VAL GLN LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 12 ALA 11 ARG 3 ASN 11 ASP 7 GLN 9 GLU > INFO_res: 7 GLY 7 HIS 6 ILE 15 LEU 2 LYS 3 MET > INFO_res: 6 PHE 9 PRO 8 SER 9 THR 5 TRP 12 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `STR70_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1513 NOE-distance constraints (0 Ambiguous NOE/s) read 1513 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1513 INTRA-RESIDUE RESTRAINTS (I=J) : 373 SEQUENTIAL RESTRAINTS (I-J)=1 : 424 BACKBONE-BACKBONE : 107 BACKBONE-SIDE CHAIN : 30 SIDE CHAIN-SIDE CHAIN : 287 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 206 BACKBONE-BACKBONE : 42 BACKBONE-SIDE CHAIN : 50 SIDE CHAIN-SIDE CHAIN : 114 LONG RANGE RESTRAINTS (I-J)>=5 : 510 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1513 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 ASN A 3 0 0.0 0.0 0.0 0.0 0.0 ASP A 4 0 0.0 0.0 0.0 0.0 0.0 THR A 5 0 0.0 0.0 0.0 0.0 0.0 PRO 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 SER 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 LEU A 10 0 0.0 0.0 0.0 0.0 0.0 TRP A 11 5 15.5 3.0 3.0 9.5 0.0 GLN A 12 7 10.0 5.0 5.0 0.0 0.0 ARG A 13 9 4.0 3.0 1.0 0.0 0.0 LEU A 14 8 7.0 4.0 1.0 2.0 0.0 LEU A 15 7 15.5 5.5 6.5 3.5 0.0 THR A 16 1 5.0 3.5 1.5 0.0 0.0 ARG A 17 0 1.5 1.0 0.0 0.5 0.0 GLY A 18 0 0.0 0.0 0.0 0.0 0.0 TRP A 19 5 19.0 1.5 0.0 17.5 0.0 GLN A 20 7 7.5 1.5 1.0 5.0 0.0 PRO A 21 0 13.5 3.5 0.0 10.0 0.0 VAL A 22 2 22.0 7.0 1.0 14.0 0.0 GLU A 23 6 17.5 7.0 5.0 5.5 0.0 ALA A 24 1 12.5 3.5 2.0 7.0 0.0 SER A 25 0 0.5 0.0 0.5 0.0 0.0 THR A 26 1 6.0 0.5 5.5 0.0 0.0 VAL A 27 3 21.5 3.5 9.5 8.5 0.0 ASP A 28 3 6.5 5.0 1.5 0.0 0.0 ASP A 29 3 9.0 4.0 5.0 0.0 0.0 TRP A 30 6 26.5 8.0 7.0 11.5 0.0 ILE A 31 7 25.5 10.0 7.0 8.5 0.0 LYS A 32 12 10.5 7.0 3.5 0.0 0.0 ARG A 33 7 9.0 7.5 1.5 0.0 0.0 VAL A 34 3 24.0 7.0 8.0 9.0 0.0 GLY A 35 0 8.0 4.0 1.5 2.5 0.0 ASP A 36 2 11.0 4.5 2.0 4.5 0.0 GLY A 37 0 16.5 5.5 1.5 9.5 0.0 VAL A 38 1 22.5 5.5 0.5 16.5 0.0 ILE A 39 5 25.0 6.0 1.5 17.5 0.0 LEU A 40 7 24.0 6.5 0.5 17.0 0.0 LEU A 41 4 17.5 5.5 1.5 10.5 0.0 SER A 42 3 6.0 2.0 0.0 4.0 0.0 SER 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 PRO A 45 0 0.0 0.0 0.0 0.0 0.0 ARG A 46 0 0.0 0.0 0.0 0.0 0.0 ARG 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 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 VAL A 51 0 0.0 0.0 0.0 0.0 0.0 SER A 52 0 0.0 0.0 0.0 0.0 0.0 ASP A 53 0 0.0 0.0 0.0 0.0 0.0 ASN A 54 0 0.0 0.0 0.0 0.0 0.0 PRO A 55 0 10.5 2.5 2.5 5.5 0.0 VAL A 56 1 6.5 4.5 1.5 0.5 0.0 MET A 57 2 5.0 3.5 1.0 0.5 0.0 ILE A 58 4 16.0 5.0 6.5 4.5 0.0 ALA A 59 1 11.0 4.5 3.5 3.0 0.0 GLU A 60 10 6.0 3.5 2.0 0.5 0.0 LEU A 61 7 22.0 5.0 10.5 6.5 0.0 LEU A 62 5 19.5 5.5 1.5 12.5 0.0 ARG A 63 6 6.0 4.0 2.0 0.0 0.0 GLU A 64 4 11.5 4.0 6.0 1.5 0.0 PHE A 65 5 14.0 4.0 2.5 7.5 0.0 PRO A 66 0 1.0 1.0 0.0 0.0 0.0 GLN A 67 9 4.5 3.5 1.0 0.0 0.0 PHE A 68 6 12.5 6.5 3.5 2.5 0.0 ASP A 69 3 4.0 4.0 0.0 0.0 0.0 TRP A 70 8 31.0 4.0 2.5 24.5 0.0 GLN A 71 5 20.0 5.5 0.0 14.5 0.0 VAL A 72 2 21.0 5.5 1.0 14.5 0.0 ALA A 73 0 15.0 5.0 0.0 10.0 0.0 VAL A 74 2 20.5 5.0 0.5 15.0 0.0 ALA A 75 0 12.5 4.0 1.0 7.5 0.0 ASP A 76 0 3.5 2.0 0.0 1.5 0.0 LEU A 77 4 5.5 5.0 0.0 0.5 0.0 GLU A 78 5 6.0 6.0 0.0 0.0 0.0 GLN A 79 9 10.5 3.5 1.5 5.5 0.0 SER A 80 1 10.0 2.0 3.0 5.0 0.0 GLU A 81 6 2.0 2.0 0.0 0.0 0.0 ALA A 82 1 6.5 3.0 3.5 0.0 0.0 ILE A 83 6 20.0 5.0 5.0 10.0 0.0 GLY A 84 1 12.0 4.5 1.5 6.0 0.0 ASP A 85 3 6.0 2.5 3.5 0.0 0.0 ARG A 86 9 7.5 6.0 1.0 0.5 0.0 PHE A 87 6 23.0 7.5 6.5 9.0 0.0 ASN A 88 2 6.5 5.5 1.0 0.0 0.0 VAL A 89 4 17.5 2.5 3.5 11.5 0.0 ARG A 90 0 0.0 0.0 0.0 0.0 0.0 ARG A 91 0 0.0 0.0 0.0 0.0 0.0 PHE A 92 0 0.0 0.0 0.0 0.0 0.0 PRO A 93 0 1.0 1.0 0.0 0.0 0.0 ALA A 94 0 12.0 3.5 0.5 8.0 0.0 THR A 95 2 17.0 6.0 0.0 11.0 0.0 LEU A 96 9 22.5 6.5 2.5 13.5 0.0 VAL A 97 2 15.0 6.0 0.5 8.5 0.0 PHE A 98 7 23.0 5.5 2.0 15.5 0.0 THR A 99 1 11.5 4.5 1.5 5.5 0.0 ASP A 100 4 7.5 4.5 2.5 0.5 0.0 GLY A 101 0 9.0 4.0 0.5 4.5 0.0 LYS A 102 17 6.5 3.0 3.0 0.5 0.0 LEU A 103 4 19.0 4.5 3.0 11.5 0.0 ARG A 104 6 12.5 6.0 0.0 6.5 0.0 GLY A 105 0 11.5 5.0 3.0 3.5 0.0 ALA A 106 0 11.0 3.0 0.0 8.0 0.0 LEU A 107 5 13.5 1.0 0.0 12.5 0.0 SER A 108 0 0.0 0.0 0.0 0.0 0.0 GLY A 109 0 0.0 0.0 0.0 0.0 0.0 ILE A 110 1 0.0 0.0 0.0 0.0 0.0 HIS A 111 0 0.0 0.0 0.0 0.0 0.0 PRO A 112 0 0.0 0.0 0.0 0.0 0.0 TRP A 113 3 14.5 3.0 3.5 8.0 0.0 ALA A 114 0 5.0 4.5 0.5 0.0 0.0 GLU A 115 4 5.5 4.5 1.0 0.0 0.0 LEU A 116 7 12.5 6.5 4.0 2.0 0.0 LEU A 117 7 8.5 6.5 1.5 0.5 0.0 THR A 118 2 5.5 4.5 1.0 0.0 0.0 LEU A 119 6 7.0 5.0 1.5 0.5 0.0 MET A 120 2 12.0 6.0 3.0 3.0 0.0 ARG A 121 7 10.5 5.5 2.5 2.5 0.0 SER A 122 3 4.0 4.0 0.0 0.0 0.0 ILE A 123 6 12.5 4.5 2.5 5.5 0.0 VAL A 124 3 11.0 5.5 1.5 4.0 0.0 ASP A 125 3 4.5 4.0 0.5 0.0 0.0 THR A 126 0 5.0 5.0 0.0 0.0 0.0 PRO A 127 0 3.0 3.0 0.0 0.0 0.0 ALA A 128 0 0.0 0.0 0.0 0.0 0.0 ALA A 129 0 0.0 0.0 0.0 0.0 0.0 GLN A 130 0 0.0 0.0 0.0 0.0 0.0 GLU A 131 0 0.0 0.0 0.0 0.0 0.0 THR A 132 0 0.0 0.0 0.0 0.0 0.0 VAL A 133 0 0.0 0.0 0.0 0.0 0.0 GLN A 134 0 0.0 0.0 0.0 0.0 0.0 LEU A 135 0 0.0 0.0 0.0 0.0 0.0 GLU A 136 0 0.0 0.0 0.0 0.0 0.0 HIS A 137 0 0.0 0.0 0.0 0.0 0.0 HIS A 138 0 0.0 0.0 0.0 0.0 0.0 HIS A 139 0 0.0 0.0 0.0 0.0 0.0 HIS A 140 0 0.0 0.0 0.0 0.0 0.0 HIS A 141 0 0.0 0.0 0.0 0.0 0.0 HIS A 142 0 0.0 0.0 0.0 0.0 0.0 TOTAL 373 1140.0 424.0 206.0 510.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_