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 `PSR293_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 24-FEB-09 2KFP > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF PSPTO_3016 FROM PSEUDOMONAS > ReadCoordsPdb(): >> TITLE 2 SYRINGAE. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 PSR293. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `PSR293_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 PSR293_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2071 ATOM records read from file > ReadCoordsPdb(): --> 2071 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2071 (674 C, 1022 H, 185 O, 187 N, 3 S, 0 Q, 0 Metals) > INFO_mol: # residues: 125 (Avg. mol. weight: 118.4) > INFO_mol: # -- M.W. : 14800.6 g/mol. (14.80 kD) Estimated RoG : 13.78 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `PSR293_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 125 > INFO_mol: Radius of Gyration : 15.5049 angstroms > INFO_mol: Center of Masses: x_cm(1.541), y_cm(-1.044), z_cm(-1.718) > INFO_res: MNRQQFIDYA QKKYDTKPDH PWEKFPDYAV FRHSDNDKWY ALLMDIPAEK > INFO_res: IGINGDKRVD VIDLKVQPEL VGSLRKKPGI YPAYHMNKEH WITVLLNGPL > INFO_res: GAKEIHSLIE DSFQLTRLEH HHHHH > INFO_res: > INFO_res: MET ASN ARG GLN GLN PHE ILE ASP TYR ALA GLN LYS > INFO_res: LYS TYR ASP THR LYS PRO ASP HIS PRO TRP GLU LYS > INFO_res: PHE PRO ASP TYR ALA VAL PHE ARG HIS SER ASP ASN > INFO_res: ASP LYS TRP TYR ALA LEU LEU MET ASP ILE PRO ALA > INFO_res: GLU LYS ILE GLY ILE ASN GLY ASP LYS ARG VAL ASP > INFO_res: VAL ILE ASP LEU LYS VAL GLN PRO GLU LEU VAL GLY > INFO_res: SER LEU ARG LYS LYS PRO GLY ILE TYR PRO ALA TYR > INFO_res: HIS MET ASN LYS GLU HIS TRP ILE THR VAL LEU LEU > INFO_res: ASN GLY PRO LEU GLY ALA LYS GLU ILE HIS SER LEU > INFO_res: ILE GLU ASP SER PHE GLN LEU THR ARG LEU GLU HIS > INFO_res: HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 6 ALA 5 ARG 5 ASN 11 ASP 5 GLN 7 GLU > INFO_res: 6 GLY 11 HIS 9 ILE 11 LEU 12 LYS 3 MET > INFO_res: 4 PHE 8 PRO 4 SER 3 THR 6 TYR 3 TRP > INFO_res: 6 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `PSR293_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1823 NOE-distance constraints (0 Ambiguous NOE/s) read 1823 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1823 INTRA-RESIDUE RESTRAINTS (I=J) : 419 SEQUENTIAL RESTRAINTS (I-J)=1 : 481 BACKBONE-BACKBONE : 117 BACKBONE-SIDE CHAIN : 72 SIDE CHAIN-SIDE CHAIN : 292 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 370 BACKBONE-BACKBONE : 73 BACKBONE-SIDE CHAIN : 86 SIDE CHAIN-SIDE CHAIN : 211 LONG RANGE RESTRAINTS (I-J)>=5 : 553 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1823 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 4 20.5 2.0 3.5 15.0 0.0 ASN A 2 0 7.0 3.0 2.0 2.0 0.0 ARG A 3 6 13.0 2.5 3.5 7.0 0.0 GLN A 4 6 9.5 4.0 5.5 0.0 0.0 GLN A 5 4 11.0 4.5 6.5 0.0 0.0 PHE A 6 4 26.0 4.5 4.0 17.5 0.0 ILE A 7 8 24.5 6.0 9.0 9.5 0.0 ASP A 8 2 10.0 4.5 5.5 0.0 0.0 TYR A 9 4 11.5 3.0 3.5 5.0 0.0 ALA A 10 1 16.0 4.5 8.0 3.5 0.0 GLN A 11 7 14.0 5.5 7.5 1.0 0.0 LYS A 12 9 8.0 5.0 3.0 0.0 0.0 LYS A 13 10 7.5 4.5 3.0 0.0 0.0 TYR A 14 4 7.5 3.0 3.5 1.0 0.0 ASP A 15 1 5.5 2.0 3.5 0.0 0.0 THR A 16 3 11.5 4.5 1.5 5.5 0.0 LYS A 17 1 6.5 5.5 0.0 1.0 0.0 PRO A 18 0 12.0 6.0 1.0 5.0 0.0 ASP A 19 0 8.5 4.5 0.0 4.0 0.0 HIS A 20 0 3.5 2.5 0.0 1.0 0.0 PRO A 21 0 5.5 3.0 0.0 2.5 0.0 TRP A 22 2 7.5 4.5 2.5 0.5 0.0 GLU A 23 5 13.0 13.0 0.0 0.0 0.0 LYS A 24 5 14.5 13.5 1.0 0.0 0.0 PHE A 25 4 9.0 6.0 3.0 0.0 0.0 PRO A 26 0 4.5 3.5 1.0 0.0 0.0 ASP A 27 1 3.5 3.0 0.5 0.0 0.0 TYR A 28 2 8.5 3.5 1.0 4.0 0.0 ALA A 29 0 11.5 3.5 1.5 6.5 0.0 VAL A 30 5 20.0 4.0 2.0 14.0 0.0 PHE A 31 2 22.0 3.5 1.5 17.0 0.0 ARG A 32 3 6.5 2.5 2.0 2.0 0.0 HIS A 33 0 4.5 3.0 1.0 0.5 0.0 SER A 34 1 4.5 4.0 0.5 0.0 0.0 ASP A 35 1 5.0 3.0 1.0 1.0 0.0 ASN A 36 0 11.0 1.5 0.5 9.0 0.0 ASP A 37 1 2.0 1.0 1.0 0.0 0.0 LYS A 38 4 1.5 1.0 0.0 0.5 0.0 TRP A 39 2 1.0 0.5 0.0 0.5 0.0 TYR A 40 0 1.5 0.5 0.0 1.0 0.0 ALA A 41 0 8.0 1.5 0.0 6.5 0.0 LEU A 42 8 12.5 2.5 4.0 6.0 0.0 LEU A 43 7 31.0 4.0 0.0 27.0 0.0 MET A 44 4 16.5 4.0 5.5 7.0 0.0 ASP A 45 0 7.0 3.0 0.0 4.0 0.0 ILE A 46 6 19.5 6.0 3.0 10.5 0.0 PRO A 47 0 14.0 6.5 5.5 2.0 0.0 ALA A 48 1 24.0 3.5 3.5 17.0 0.0 GLU A 49 2 9.5 3.5 5.5 0.5 0.0 LYS A 50 3 12.5 6.0 5.0 1.5 0.0 ILE A 51 10 26.5 7.0 7.0 12.5 0.0 GLY A 52 0 5.0 3.5 1.5 0.0 0.0 ILE A 53 12 24.5 5.0 10.0 9.5 0.0 ASN A 54 3 6.5 5.5 0.0 1.0 0.0 GLY A 55 1 6.0 2.0 3.0 1.0 0.0 ASP A 56 1 5.5 3.0 0.5 2.0 0.0 LYS A 57 4 10.5 4.5 2.5 3.5 0.0 ARG A 58 4 10.0 6.0 0.0 4.0 0.0 VAL A 59 4 21.0 6.5 2.0 12.5 0.0 ASP A 60 2 14.0 6.0 0.5 7.5 0.0 VAL A 61 3 22.5 5.5 0.5 16.5 0.0 ILE A 62 5 21.5 2.5 1.5 17.5 0.0 ASP A 63 0 0.0 0.0 0.0 0.0 0.0 LEU A 64 4 13.5 1.0 3.0 9.5 0.0 LYS A 65 5 15.0 5.5 0.0 9.5 0.0 VAL A 66 4 26.0 7.5 5.0 13.5 0.0 GLN A 67 11 20.5 4.5 10.0 6.0 0.0 PRO A 68 0 5.5 3.0 2.5 0.0 0.0 GLU A 69 3 7.5 4.5 3.0 0.0 0.0 LEU A 70 8 19.0 6.0 13.0 0.0 0.0 VAL A 71 5 24.5 5.5 11.5 7.5 0.0 GLY A 72 0 7.0 3.0 4.0 0.0 0.0 SER A 73 1 8.5 1.5 7.0 0.0 0.0 LEU A 74 8 18.0 3.5 6.5 8.0 0.0 ARG A 75 12 24.5 3.5 7.0 14.0 0.0 LYS A 76 17 11.5 5.5 6.0 0.0 0.0 LYS A 77 6 10.0 4.5 4.5 1.0 0.0 PRO A 78 0 3.5 1.5 1.0 1.0 0.0 GLY A 79 0 6.5 2.5 1.0 3.0 0.0 ILE A 80 9 18.0 4.0 4.0 10.0 0.0 TYR A 81 2 17.5 6.0 1.0 10.5 0.0 PRO A 82 0 15.0 3.0 1.0 11.0 0.0 ALA A 83 0 0.0 0.0 0.0 0.0 0.0 TYR A 84 1 5.0 0.0 0.0 5.0 0.0 HIS A 85 0 0.0 0.0 0.0 0.0 0.0 MET A 86 0 0.0 0.0 0.0 0.0 0.0 ASN A 87 0 2.0 0.5 1.5 0.0 0.0 LYS A 88 2 8.0 1.0 2.0 5.0 0.0 GLU A 89 3 8.0 5.0 0.5 2.5 0.0 HIS A 90 0 8.0 7.0 0.0 1.0 0.0 TRP A 91 1 7.5 4.0 1.5 2.0 0.0 ILE A 92 6 18.0 4.5 1.5 12.0 0.0 THR A 93 3 6.0 3.0 0.0 3.0 0.0 VAL A 94 1 7.0 2.0 0.5 4.5 0.0 LEU A 95 10 22.5 3.5 6.0 13.0 0.0 LEU A 96 5 25.5 3.0 0.5 22.0 0.0 ASN A 97 3 5.0 2.5 2.0 0.5 0.0 GLY A 98 0 4.0 1.5 2.5 0.0 0.0 PRO A 99 0 6.0 2.5 1.5 2.0 0.0 LEU A 100 9 18.5 7.0 3.5 8.0 0.0 GLY A 101 0 11.5 8.0 3.5 0.0 0.0 ALA A 102 1 13.0 5.5 5.5 2.0 0.0 LYS A 103 6 6.5 4.0 2.5 0.0 0.0 GLU A 104 4 12.0 3.5 8.5 0.0 0.0 ILE A 105 10 29.0 4.5 13.0 11.5 0.0 HIS A 106 3 11.5 3.5 6.5 1.5 0.0 SER A 107 1 9.5 3.5 6.0 0.0 0.0 LEU A 108 7 14.5 6.0 5.5 3.0 0.0 ILE A 109 10 33.5 6.5 12.5 14.5 0.0 GLU A 110 3 12.0 5.0 7.0 0.0 0.0 ASP A 111 1 7.5 3.5 4.0 0.0 0.0 SER A 112 2 13.5 2.0 6.5 5.0 0.0 PHE A 113 2 7.5 3.0 4.5 0.0 0.0 GLN A 114 3 7.5 3.5 4.0 0.0 0.0 LEU A 115 11 21.0 5.0 4.0 12.0 0.0 THR A 116 3 10.5 6.0 2.5 2.0 0.0 ARG A 117 8 8.5 4.5 3.5 0.5 0.0 LEU A 118 8 15.0 5.5 0.5 9.0 0.0 GLU A 119 5 7.5 7.0 0.0 0.5 0.0 HIS A 120 0 5.5 5.0 0.5 0.0 0.0 HIS A 121 0 2.0 2.0 0.0 0.0 0.0 HIS A 122 0 2.0 2.0 0.0 0.0 0.0 HIS A 123 0 1.5 1.5 0.0 0.0 0.0 HIS A 124 0 0.5 0.5 0.0 0.0 0.0 HIS A 125 0 0.0 0.0 0.0 0.0 0.0 TOTAL 419 1404.0 481.0 370.0 553.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_