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 `DHR8C_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 27-MAY-10 2KYI > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF DSY0195(21-82) PROTEIN FROM > ReadCoordsPdb(): >> TITLE 2 DESULFITOBACTERIUM HAFNIENSE. NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET DHR8C > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `DHR8C_NMR_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 DHR8C_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2290 ATOM records read from file > ReadCoordsPdb(): --> 2290 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2290 (720 C, 1162 H, 208 O, 198 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 142 (Avg. mol. weight: 112.6) > INFO_mol: # -- M.W. : 15984.1 g/mol. (15.98 kD) Estimated RoG : 14.46 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `DHR8C_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 142 > INFO_mol: Radius of Gyration : 15.0116 angstroms > INFO_mol: Center of Masses: x_cm(-0.009), y_cm(0.163), z_cm(0.572) > INFO_res: MDNRQFLSLT GVSKVQSFDP KEILLETIQG VLSIKGEKLG IKHLDLKAGQ > INFO_res: VEVEGLIDAL VYPLEHHHHH HMDNRQFLSL TGVSKVQSFD PKEILLETIQ > INFO_res: GVLSIKGEKL GIKHLDLKAG QVEVEGLIDA LVYPLEHHHH HH > INFO_res: > INFO_res: MET ASP ASN ARG GLN PHE LEU SER LEU THR GLY VAL > INFO_res: SER LYS VAL GLN SER PHE ASP PRO LYS GLU ILE LEU > INFO_res: LEU GLU THR ILE GLN GLY VAL LEU SER ILE LYS GLY > INFO_res: GLU LYS LEU GLY ILE LYS HIS LEU ASP LEU LYS ALA > INFO_res: GLY GLN VAL GLU VAL GLU GLY LEU ILE ASP ALA LEU > INFO_res: VAL TYR PRO LEU GLU HIS HIS HIS HIS HIS HIS MET > INFO_res: ASP ASN ARG GLN PHE LEU SER LEU THR GLY VAL SER > INFO_res: LYS VAL GLN SER PHE ASP PRO LYS GLU ILE LEU LEU > INFO_res: GLU THR ILE GLN GLY VAL LEU SER ILE LYS GLY GLU > INFO_res: LYS LEU GLY ILE LYS HIS LEU ASP LEU LYS ALA GLY > INFO_res: GLN VAL GLU VAL GLU GLY LEU ILE ASP ALA LEU VAL > INFO_res: TYR PRO LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 4 ALA 2 ARG 2 ASN 8 ASP 8 GLN 12 GLU > INFO_res: 12 GLY 14 HIS 10 ILE 22 LEU 12 LYS 2 MET > INFO_res: 4 PHE 4 PRO 8 SER 4 THR 2 TYR 12 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `DHR8C_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 822 NOE-distance constraints (0 Ambiguous NOE/s) read 822 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 822 INTRA-RESIDUE RESTRAINTS (I=J) : 249 SEQUENTIAL RESTRAINTS (I-J)=1 : 204 BACKBONE-BACKBONE : 74 BACKBONE-SIDE CHAIN : 0 SIDE CHAIN-SIDE CHAIN : 130 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 11 BACKBONE-BACKBONE : 2 BACKBONE-SIDE CHAIN : 5 SIDE CHAIN-SIDE CHAIN : 4 LONG RANGE RESTRAINTS (I-J)>=5 : 358 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 822 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 2 1.5 1.5 0.0 0.0 0.0 ASP A 2 2 3.0 3.0 0.0 0.0 0.0 ASN A 3 3 7.0 3.5 0.0 3.5 0.0 ARG A 4 13 13.5 4.0 0.0 9.5 0.0 GLN A 5 1 9.5 4.0 0.0 5.5 0.0 PHE A 6 2 9.5 3.5 0.0 6.0 0.0 LEU A 7 5 10.0 3.0 0.0 7.0 0.0 SER A 8 1 7.5 3.0 0.0 4.5 0.0 LEU A 9 8 13.5 5.0 1.0 7.5 0.0 THR A 10 1 9.0 4.5 0.0 4.5 0.0 GLY A 11 0 2.5 1.5 0.0 1.0 0.0 VAL A 12 3 10.5 2.5 1.0 7.0 0.0 SER A 13 2 9.0 4.0 0.0 5.0 0.0 LYS A 14 8 8.5 3.0 0.0 5.5 0.0 VAL A 15 3 6.5 2.5 0.0 4.0 0.0 GLN A 16 8 17.0 3.5 0.0 13.5 0.0 SER A 17 0 12.5 4.0 0.0 8.5 0.0 PHE A 18 0 8.0 2.0 0.0 6.0 0.0 ASP A 19 0 0.0 0.0 0.0 0.0 0.0 PRO A 20 0 5.0 1.0 0.0 4.0 0.0 LYS A 21 13 5.0 4.0 0.0 1.0 0.0 GLU A 22 3 11.0 6.0 0.0 5.0 0.0 ILE A 23 8 21.0 5.5 0.0 15.5 0.0 LEU A 24 8 22.0 4.5 0.0 17.5 0.0 LEU A 25 9 17.0 5.0 0.0 12.0 0.0 GLU A 26 4 18.0 5.0 0.0 13.0 0.0 THR A 27 3 17.0 2.5 2.0 12.5 0.0 ILE A 28 9 2.5 2.0 0.0 0.5 0.0 GLN A 29 4 3.0 3.0 0.0 0.0 0.0 GLY A 30 0 3.5 3.0 0.5 0.0 0.0 VAL A 31 5 16.5 4.0 1.5 11.0 0.0 LEU A 32 7 16.0 5.5 0.0 10.5 0.0 SER A 33 0 12.5 4.5 0.0 8.0 0.0 ILE A 34 9 19.0 3.5 0.0 15.5 0.0 LYS A 35 12 16.5 5.0 1.0 10.5 0.0 GLY A 36 0 10.5 4.0 1.5 5.0 0.0 GLU A 37 4 10.0 3.0 0.0 7.0 0.0 LYS A 38 8 9.0 3.0 0.0 6.0 0.0 LEU A 39 8 20.5 3.0 2.5 15.0 0.0 GLY A 40 0 3.0 2.0 0.0 1.0 0.0 ILE A 41 0 0.0 0.0 0.0 0.0 0.0 LYS A 42 0 0.0 0.0 0.0 0.0 0.0 HIS A 43 0 0.0 0.0 0.0 0.0 0.0 LEU A 44 0 0.0 0.0 0.0 0.0 0.0 ASP A 45 0 0.0 0.0 0.0 0.0 0.0 LEU A 46 6 3.5 1.0 0.0 2.5 0.0 LYS A 47 8 3.0 3.0 0.0 0.0 0.0 ALA A 48 1 3.5 3.5 0.0 0.0 0.0 GLY A 49 0 2.0 1.5 0.0 0.5 0.0 GLN A 50 7 7.0 3.0 0.0 4.0 0.0 VAL A 51 5 9.0 4.5 0.0 4.5 0.0 GLU A 52 4 7.0 3.5 0.0 3.5 0.0 VAL A 53 2 5.5 3.5 0.0 2.0 0.0 GLU A 54 1 8.5 3.0 0.0 5.5 0.0 GLY A 55 0 10.0 2.0 0.0 8.0 0.0 LEU A 56 8 25.5 3.0 0.0 22.5 0.0 ILE A 57 8 16.0 4.5 0.0 11.5 0.0 ASP A 58 0 9.5 4.5 0.0 5.0 0.0 ALA A 59 1 9.0 4.0 0.0 5.0 0.0 LEU A 60 7 9.5 3.5 0.0 6.0 0.0 VAL A 61 4 7.0 3.5 0.0 3.5 0.0 TYR A 62 1 6.5 1.5 0.0 5.0 0.0 PRO A 63 0 2.0 2.0 0.0 0.0 0.0 LEU A 64 7 4.5 4.5 0.0 0.0 0.0 GLU A 65 3 4.0 4.0 0.0 0.0 0.0 HIS A 66 0 1.5 1.5 0.0 0.0 0.0 HIS A 67 0 0.0 0.0 0.0 0.0 0.0 HIS A 68 0 0.0 0.0 0.0 0.0 0.0 HIS A 69 0 0.0 0.0 0.0 0.0 0.0 HIS A 70 0 1.0 1.0 0.0 0.0 0.0 HIS A 71 0 1.0 1.0 0.0 0.0 0.0 MET B 72 0 0.0 0.0 0.0 0.0 0.0 ASP 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 ARG B 75 0 0.0 0.0 0.0 0.0 0.0 GLN B 76 0 0.0 0.0 0.0 0.0 0.0 PHE B 77 0 0.0 0.0 0.0 0.0 0.0 LEU B 78 0 0.0 0.0 0.0 0.0 0.0 SER B 79 0 0.0 0.0 0.0 0.0 0.0 LEU B 80 0 0.0 0.0 0.0 0.0 0.0 THR B 81 0 0.0 0.0 0.0 0.0 0.0 GLY B 82 0 0.0 0.0 0.0 0.0 0.0 VAL B 83 0 0.0 0.0 0.0 0.0 0.0 SER B 84 0 0.0 0.0 0.0 0.0 0.0 LYS 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 GLN B 87 0 0.0 0.0 0.0 0.0 0.0 SER B 88 0 0.0 0.0 0.0 0.0 0.0 PHE B 89 0 0.0 0.0 0.0 0.0 0.0 ASP B 90 0 0.0 0.0 0.0 0.0 0.0 PRO B 91 0 0.0 0.0 0.0 0.0 0.0 LYS B 92 0 0.0 0.0 0.0 0.0 0.0 GLU B 93 0 0.0 0.0 0.0 0.0 0.0 ILE B 94 0 0.0 0.0 0.0 0.0 0.0 LEU B 95 0 0.0 0.0 0.0 0.0 0.0 LEU B 96 0 0.0 0.0 0.0 0.0 0.0 GLU B 97 0 0.0 0.0 0.0 0.0 0.0 THR B 98 0 0.0 0.0 0.0 0.0 0.0 ILE B 99 0 0.0 0.0 0.0 0.0 0.0 GLN B 100 0 0.0 0.0 0.0 0.0 0.0 GLY B 101 0 0.0 0.0 0.0 0.0 0.0 VAL B 102 0 0.0 0.0 0.0 0.0 0.0 LEU B 103 0 0.0 0.0 0.0 0.0 0.0 SER B 104 0 0.0 0.0 0.0 0.0 0.0 ILE B 105 0 0.0 0.0 0.0 0.0 0.0 LYS B 106 0 0.0 0.0 0.0 0.0 0.0 GLY B 107 0 0.0 0.0 0.0 0.0 0.0 GLU B 108 0 0.0 0.0 0.0 0.0 0.0 LYS B 109 0 0.0 0.0 0.0 0.0 0.0 LEU B 110 0 0.0 0.0 0.0 0.0 0.0 GLY B 111 0 0.0 0.0 0.0 0.0 0.0 ILE B 112 0 0.0 0.0 0.0 0.0 0.0 LYS B 113 0 0.0 0.0 0.0 0.0 0.0 HIS B 114 0 0.0 0.0 0.0 0.0 0.0 LEU B 115 0 0.0 0.0 0.0 0.0 0.0 ASP B 116 0 0.0 0.0 0.0 0.0 0.0 LEU B 117 0 0.0 0.0 0.0 0.0 0.0 LYS B 118 0 0.0 0.0 0.0 0.0 0.0 ALA B 119 0 0.0 0.0 0.0 0.0 0.0 GLY B 120 0 0.0 0.0 0.0 0.0 0.0 GLN B 121 0 0.0 0.0 0.0 0.0 0.0 VAL B 122 0 0.0 0.0 0.0 0.0 0.0 GLU B 123 0 0.0 0.0 0.0 0.0 0.0 VAL B 124 0 0.0 0.0 0.0 0.0 0.0 GLU B 125 0 0.0 0.0 0.0 0.0 0.0 GLY B 126 0 0.0 0.0 0.0 0.0 0.0 LEU B 127 0 0.0 0.0 0.0 0.0 0.0 ILE B 128 0 0.0 0.0 0.0 0.0 0.0 ASP B 129 0 0.0 0.0 0.0 0.0 0.0 ALA B 130 0 0.0 0.0 0.0 0.0 0.0 LEU B 131 0 0.0 0.0 0.0 0.0 0.0 VAL B 132 0 0.0 0.0 0.0 0.0 0.0 TYR B 133 0 0.0 0.0 0.0 0.0 0.0 PRO B 134 0 0.0 0.0 0.0 0.0 0.0 LEU B 135 0 0.0 0.0 0.0 0.0 0.0 GLU B 136 0 0.0 0.0 0.0 0.0 0.0 HIS B 137 0 0.0 0.0 0.0 0.0 0.0 HIS B 138 0 0.0 0.0 0.0 0.0 0.0 HIS B 139 0 0.0 0.0 0.0 0.0 0.0 HIS B 140 0 0.0 0.0 0.0 0.0 0.0 HIS B 141 0 0.0 0.0 0.0 0.0 0.0 HIS B 142 0 0.0 0.0 0.0 0.0 0.0 TOTAL 249 573.0 204.0 11.0 358.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_