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 `SSR10_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS 23-MAY-07 2JPU > ReadCoordsPdb(): >> TITLE SOLUTION STRUCTURE OF NESG TARGET SSR10, ORF C02003 PROTEIN > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: ORF C02003 PROTEIN; > ReadCoordsPdb(): >> COMPND 3 CHAIN: A; 1 > ReadCoordsPdb(): Counting models in file `SSR10_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 SSR10_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2139 ATOM records read from file > ReadCoordsPdb(): --> 2139 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2139 (679 C, 1075 H, 199 O, 184 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 129 (Avg. mol. weight: 116.8) > INFO_mol: # -- M.W. : 15063.9 g/mol. (15.06 kD) Estimated RoG : 13.95 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SSR10_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 129 > INFO_mol: Radius of Gyration : 15.3643 angstroms > INFO_mol: Center of Masses: x_cm(0.255), y_cm(-0.124), z_cm(0.058) > INFO_res: MSISTSAEVY YEEAEEFLSK GDLVQACEKY YKAAEEAIKL LVIENNLKEI > INFO_res: TNNVKNKGRW KSENLFKASK LLRSNNTEIP ILWKSAWTLH VEGFHELSLN > INFO_res: EKEVKKLKED VRKLVIFAVN SLEHHHHHH > INFO_res: > INFO_res: MET SER ILE SER THR SER ALA GLU VAL TYR TYR GLU > INFO_res: GLU ALA GLU GLU PHE LEU SER LYS GLY ASP LEU VAL > INFO_res: GLN ALA CYS GLU LYS TYR TYR LYS ALA ALA GLU GLU > INFO_res: ALA ILE LYS LEU LEU VAL ILE GLU ASN ASN LEU LYS > INFO_res: GLU ILE THR ASN ASN VAL LYS ASN LYS GLY ARG TRP > INFO_res: LYS SER GLU ASN LEU PHE LYS ALA SER LYS LEU LEU > INFO_res: ARG SER ASN ASN THR GLU ILE PRO ILE LEU TRP LYS > INFO_res: SER ALA TRP THR LEU HIS VAL GLU GLY PHE HIS GLU > INFO_res: LEU SER LEU ASN GLU LYS GLU VAL LYS LYS LEU LYS > INFO_res: GLU ASP VAL ARG LYS LEU VAL ILE PHE ALA VAL ASN > INFO_res: SER LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 9 ALA 3 ARG 10 ASN 2 ASP 1 CYS 1 GLN > INFO_res: 18 GLU 3 GLY 8 HIS 7 ILE 15 LEU 16 LYS > INFO_res: 1 MET 4 PHE 1 PRO 10 SER 4 THR 4 TYR > INFO_res: 3 TRP 9 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `SSR10_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1661 NOE-distance constraints (0 Ambiguous NOE/s) read 1661 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1661 INTRA-RESIDUE RESTRAINTS (I=J) : 542 SEQUENTIAL RESTRAINTS (I-J)=1 : 444 BACKBONE-BACKBONE : 131 BACKBONE-SIDE CHAIN : 18 SIDE CHAIN-SIDE CHAIN : 295 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 362 BACKBONE-BACKBONE : 144 BACKBONE-SIDE CHAIN : 129 SIDE CHAIN-SIDE CHAIN : 89 LONG RANGE RESTRAINTS (I-J)>=5 : 313 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1661 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 SER A 2 0 0.0 0.0 0.0 0.0 0.0 ILE A 3 4 4.0 3.5 0.5 0.0 0.0 SER A 4 0 6.5 5.5 0.0 1.0 0.0 THR A 5 1 10.5 4.0 4.5 2.0 0.0 SER A 6 3 7.0 3.5 3.5 0.0 0.0 ALA A 7 0 12.0 2.0 3.0 7.0 0.0 GLU A 8 6 10.0 2.0 4.0 4.0 0.0 VAL A 9 2 10.5 4.5 5.0 1.0 0.0 TYR A 10 2 22.0 4.5 5.5 12.0 0.0 TYR A 11 2 16.5 4.5 3.0 9.0 0.0 GLU A 12 3 9.5 4.5 4.5 0.5 0.0 GLU A 13 9 8.5 5.0 3.5 0.0 0.0 ALA A 14 0 14.5 4.0 4.0 6.5 0.0 GLU A 15 7 6.0 1.5 4.5 0.0 0.0 GLU A 16 8 7.5 4.0 3.5 0.0 0.0 PHE A 17 2 17.0 5.0 5.0 7.0 0.0 LEU A 18 7 14.0 5.5 5.0 3.5 0.0 SER A 19 0 5.5 4.0 1.5 0.0 0.0 LYS A 20 5 7.5 2.5 5.0 0.0 0.0 GLY A 21 0 4.0 2.5 1.5 0.0 0.0 ASP A 22 3 8.0 2.5 3.5 2.0 0.0 LEU A 23 7 15.5 5.0 2.5 8.0 0.0 VAL A 24 4 11.0 7.0 3.0 1.0 0.0 GLN A 25 13 8.0 6.0 1.0 1.0 0.0 ALA A 26 0 15.0 4.0 4.0 7.0 0.0 CYS A 27 3 8.0 4.0 3.5 0.5 0.0 GLU A 28 3 4.5 2.5 2.0 0.0 0.0 LYS A 29 0 8.5 2.5 1.5 4.5 0.0 TYR A 30 0 8.5 2.5 3.5 2.5 0.0 TYR A 31 3 11.5 2.0 5.5 4.0 0.0 LYS A 32 10 8.0 3.5 1.5 3.0 0.0 ALA A 33 0 17.5 3.0 4.0 10.5 0.0 ALA A 34 0 11.5 1.5 3.0 7.0 0.0 GLU A 35 9 13.0 2.5 4.5 6.0 0.0 GLU A 36 6 13.5 4.5 2.0 7.0 0.0 ALA A 37 0 14.0 3.0 3.5 7.5 0.0 ILE A 38 9 13.0 2.0 3.0 8.0 0.0 LYS A 39 0 5.5 2.5 2.5 0.5 0.0 LEU A 40 10 9.5 3.0 4.0 2.5 0.0 LEU A 41 8 17.5 4.5 8.0 5.0 0.0 VAL A 42 2 18.0 5.0 2.0 11.0 0.0 ILE A 43 8 9.0 4.5 2.5 2.0 0.0 GLU A 44 9 4.5 4.5 0.0 0.0 0.0 ASN A 45 3 11.0 3.0 6.5 1.5 0.0 ASN A 46 6 2.0 1.5 0.5 0.0 0.0 LEU A 47 7 10.0 3.0 1.0 6.0 0.0 LYS A 48 9 9.0 4.0 5.0 0.0 0.0 GLU A 49 10 9.5 4.5 3.5 1.5 0.0 ILE A 50 7 18.0 5.5 3.0 9.5 0.0 THR A 51 3 7.0 4.0 2.5 0.5 0.0 ASN A 52 0 8.5 1.5 7.0 0.0 0.0 ASN A 53 4 5.0 1.5 3.0 0.5 0.0 VAL A 54 2 9.5 3.5 3.0 3.0 0.0 LYS A 55 7 6.5 6.0 0.5 0.0 0.0 ASN A 56 3 7.0 6.0 1.0 0.0 0.0 LYS A 57 10 5.0 5.0 0.0 0.0 0.0 GLY A 58 0 4.0 4.0 0.0 0.0 0.0 ARG A 59 4 4.5 4.5 0.0 0.0 0.0 TRP A 60 4 18.0 5.0 0.0 13.0 0.0 LYS A 61 6 5.5 4.0 1.5 0.0 0.0 SER A 62 5 3.0 2.5 0.5 0.0 0.0 GLU A 63 3 5.5 3.5 2.0 0.0 0.0 ASN A 64 6 10.0 5.5 3.5 1.0 0.0 LEU A 65 7 14.0 4.0 2.0 8.0 0.0 PHE A 66 4 4.5 3.5 1.0 0.0 0.0 LYS A 67 9 11.0 3.5 4.5 3.0 0.0 ALA A 68 0 8.0 2.0 2.5 3.5 0.0 SER A 69 3 8.5 2.0 2.0 4.5 0.0 LYS A 70 9 6.0 4.5 1.5 0.0 0.0 LEU A 71 8 9.0 5.5 2.0 1.5 0.0 LEU A 72 6 10.0 3.0 2.0 5.0 0.0 ARG A 73 10 5.5 3.0 2.5 0.0 0.0 SER A 74 0 3.5 3.0 0.5 0.0 0.0 ASN A 75 6 4.0 2.0 2.0 0.0 0.0 ASN A 76 0 6.0 3.0 3.0 0.0 0.0 THR A 77 3 5.5 3.0 2.5 0.0 0.0 GLU A 78 9 9.5 3.0 6.5 0.0 0.0 ILE A 79 4 14.0 4.5 6.0 3.5 0.0 PRO A 80 0 7.5 4.5 1.5 1.5 0.0 ILE A 81 10 9.5 4.0 5.5 0.0 0.0 LEU A 82 8 23.0 6.0 7.0 10.0 0.0 TRP A 83 2 19.0 4.0 4.0 11.0 0.0 LYS A 84 8 6.5 2.0 4.5 0.0 0.0 SER A 85 3 6.5 3.5 2.0 1.0 0.0 ALA A 86 0 11.0 2.5 3.0 5.5 0.0 TRP A 87 4 6.5 1.5 4.0 1.0 0.0 THR A 88 1 7.5 2.5 4.5 0.5 0.0 LEU A 89 4 9.0 3.0 2.0 4.0 0.0 HIS A 90 4 5.0 4.0 1.0 0.0 0.0 VAL A 91 2 8.5 4.5 4.0 0.0 0.0 GLU A 92 2 3.5 2.5 1.0 0.0 0.0 GLY A 93 0 1.0 1.0 0.0 0.0 0.0 PHE A 94 2 3.0 3.0 0.0 0.0 0.0 HIS A 95 3 3.0 3.0 0.0 0.0 0.0 GLU A 96 0 1.0 1.0 0.0 0.0 0.0 LEU A 97 11 4.5 4.0 0.5 0.0 0.0 SER A 98 2 6.0 5.0 0.0 1.0 0.0 LEU A 99 7 6.0 5.0 0.5 0.5 0.0 ASN A 100 2 8.0 5.5 2.0 0.5 0.0 GLU A 101 4 15.5 4.5 4.5 6.5 0.0 LYS A 102 11 7.0 4.5 2.5 0.0 0.0 GLU A 103 3 8.5 5.5 3.0 0.0 0.0 VAL A 104 3 11.5 5.5 5.0 1.0 0.0 LYS A 105 10 8.5 3.5 5.0 0.0 0.0 LYS A 106 5 5.0 2.5 2.5 0.0 0.0 LEU A 107 6 9.5 2.5 4.5 2.5 0.0 LYS A 108 5 7.5 3.0 4.5 0.0 0.0 GLU A 109 3 7.5 2.5 5.0 0.0 0.0 ASP A 110 2 9.0 2.5 4.0 2.5 0.0 VAL A 111 2 19.0 3.5 5.5 10.0 0.0 ARG A 112 4 11.5 3.0 6.5 2.0 0.0 LYS A 113 9 9.0 2.0 2.5 4.5 0.0 LEU A 114 9 17.5 4.5 4.5 8.5 0.0 VAL A 115 3 19.0 4.5 5.5 9.0 0.0 ILE A 116 10 11.5 5.0 6.5 0.0 0.0 PHE A 117 2 13.5 6.0 4.5 3.0 0.0 ALA A 118 0 12.0 2.5 4.5 5.0 0.0 VAL A 119 4 8.0 3.0 3.5 1.5 0.0 ASN A 120 3 9.0 4.5 4.5 0.0 0.0 SER A 121 2 7.5 5.0 2.5 0.0 0.0 LEU A 122 4 7.5 5.0 1.5 1.0 0.0 GLU A 123 5 3.5 3.0 0.5 0.0 0.0 HIS A 124 5 1.0 1.0 0.0 0.0 0.0 HIS A 125 5 0.5 0.5 0.0 0.0 0.0 HIS A 126 3 0.5 0.5 0.0 0.0 0.0 HIS A 127 0 0.0 0.0 0.0 0.0 0.0 HIS A 128 0 0.0 0.0 0.0 0.0 0.0 HIS A 129 0 0.0 0.0 0.0 0.0 0.0 TOTAL 542 1119.0 444.0 362.0 313.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_