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 `LKR112_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 114 MET LYS ASN THR GLY ASP GLU VAL VAL ALA ILE ILE SER 1 > ReadCoordsPdb(): Counting models in file `LKR112_R3Cons_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 LKR112_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1795 ATOM records read from file > ReadCoordsPdb(): --> 1795 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1795 (558 C, 897 H, 172 O, 164 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 114 (Avg. mol. weight: 112.1) > INFO_mol: # -- M.W. : 12783.3 g/mol. (12.78 kD) Estimated RoG : 13.31 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `LKR112_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 114 > INFO_mol: Radius of Gyration : 14.6719 angstroms > INFO_mol: Center of Masses: x_cm(15.226), y_cm(-6.963), z_cm(18.737) > INFO_res: MKNTGDEVVA IISQNGKVIR EIPLTGHKGN EQFTIKGKGA QYNLMEVDGE > INFO_res: RIRIKEDNSP DQVGVKMGWK SKAGDTIVCL PHKVFVEIKS TQKDSKDPDT > INFO_res: DLIVPNLEHH HHHH > INFO_res: > INFO_res: MET LYS ASN THR GLY ASP GLU VAL VAL ALA ILE ILE > INFO_res: SER GLN ASN GLY LYS VAL ILE ARG GLU ILE PRO LEU > INFO_res: THR GLY HIS LYS GLY ASN GLU GLN PHE THR ILE LYS > INFO_res: GLY LYS GLY ALA GLN TYR ASN LEU MET GLU VAL ASP > INFO_res: GLY GLU ARG ILE ARG ILE LYS GLU ASP ASN SER PRO > INFO_res: ASP GLN VAL GLY VAL LYS MET GLY TRP LYS SER LYS > INFO_res: ALA GLY ASP THR ILE VAL CYS LEU PRO HIS LYS VAL > INFO_res: PHE VAL GLU ILE LYS SER THR GLN LYS ASP SER LYS > INFO_res: ASP PRO ASP THR ASP LEU ILE VAL PRO ASN LEU GLU > INFO_res: HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 3 ALA 3 ARG 6 ASN 9 ASP 1 CYS 5 GLN > INFO_res: 8 GLU 10 GLY 8 HIS 10 ILE 5 LEU 13 LYS > INFO_res: 3 MET 2 PHE 5 PRO 5 SER 6 THR 1 TYR > INFO_res: 1 TRP 10 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `LKR112_R3Cons_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 2542 NOE-distance constraints (0 Ambiguous NOE/s) read 2542 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 2542 INTRA-RESIDUE RESTRAINTS (I=J) : 485 SEQUENTIAL RESTRAINTS (I-J)=1 : 722 BACKBONE-BACKBONE : 169 BACKBONE-SIDE CHAIN : 136 SIDE CHAIN-SIDE CHAIN : 417 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 314 BACKBONE-BACKBONE : 46 BACKBONE-SIDE CHAIN : 51 SIDE CHAIN-SIDE CHAIN : 217 LONG RANGE RESTRAINTS (I-J)>=5 : 1021 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 2542 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 1 0.0 0.0 0.0 0.0 0.0 ASN A 3 4 2.0 2.0 0.0 0.0 0.0 THR A 4 2 5.0 4.0 1.0 0.0 0.0 GLY A 5 0 4.5 4.5 0.0 0.0 0.0 ASP A 6 1 6.5 5.0 1.5 0.0 0.0 GLU A 7 5 21.0 9.0 0.0 12.0 0.0 VAL A 8 4 39.0 11.5 1.0 26.5 0.0 VAL A 9 2 33.0 9.0 1.0 23.0 0.0 ALA A 10 1 30.0 7.0 2.0 21.0 0.0 ILE A 11 12 33.0 7.0 2.5 23.5 0.0 ILE A 12 9 37.0 8.5 1.5 27.0 0.0 SER A 13 0 27.5 8.5 3.0 16.0 0.0 GLN A 14 11 37.0 12.5 3.0 21.5 0.0 ASN A 15 5 26.0 12.0 3.5 10.5 0.0 GLY A 16 0 6.0 4.0 1.5 0.5 0.0 LYS A 17 4 14.5 5.5 9.0 0.0 0.0 VAL A 18 5 21.5 12.0 3.5 6.0 0.0 ILE A 19 10 39.0 15.0 3.0 21.0 0.0 ARG A 20 8 31.5 14.0 7.5 10.0 0.0 GLU A 21 5 24.0 11.0 1.0 12.0 0.0 ILE A 22 12 32.5 13.0 7.5 12.0 0.0 PRO A 23 0 18.5 9.5 1.0 8.0 0.0 LEU A 24 10 41.5 4.5 5.0 32.0 0.0 THR A 25 3 25.5 7.0 2.0 16.5 0.0 GLY A 26 0 6.5 4.5 0.0 2.0 0.0 HIS A 27 3 17.5 3.5 8.0 6.0 0.0 LYS A 28 14 10.0 8.0 0.0 2.0 0.0 GLY A 29 0 10.0 9.0 0.0 1.0 0.0 ASN A 30 6 20.5 8.5 3.0 9.0 0.0 GLU A 31 3 23.0 9.0 5.0 9.0 0.0 GLN A 32 7 23.5 9.0 2.5 12.0 0.0 PHE A 33 7 40.0 8.0 6.0 26.0 0.0 THR A 34 3 19.5 6.5 4.0 9.0 0.0 ILE A 35 11 31.5 6.0 4.5 21.0 0.0 LYS A 36 13 13.0 7.0 4.0 2.0 0.0 GLY A 37 0 11.5 5.5 3.0 3.0 0.0 LYS A 38 8 7.5 5.5 2.0 0.0 0.0 GLY A 39 0 7.5 5.0 2.5 0.0 0.0 ALA A 40 0 4.5 2.5 0.5 1.5 0.0 GLN A 41 8 19.5 4.5 7.5 7.5 0.0 TYR A 42 6 28.0 5.5 4.0 18.5 0.0 ASN A 43 3 26.5 4.5 0.5 21.5 0.0 LEU A 44 11 40.0 5.5 3.5 31.0 0.0 MET A 45 9 35.0 6.0 1.5 27.5 0.0 GLU A 46 3 27.0 7.5 2.5 17.0 0.0 VAL A 47 5 44.0 8.0 3.0 33.0 0.0 ASP A 48 0 26.0 6.5 9.0 10.5 0.0 GLY A 49 0 12.0 5.5 2.0 4.5 0.0 GLU A 50 0 18.0 6.0 0.5 11.5 0.0 ARG A 51 10 29.5 8.0 6.5 15.0 0.0 ILE A 52 6 41.0 8.5 2.5 30.0 0.0 ARG A 53 5 24.5 7.0 4.0 13.5 0.0 ILE A 54 7 29.0 3.5 4.0 21.5 0.0 LYS A 55 3 20.5 4.5 4.0 12.0 0.0 GLU A 56 4 23.0 8.0 1.5 13.5 0.0 ASP A 57 0 21.5 6.5 3.5 11.5 0.0 ASN A 58 1 18.0 3.0 3.5 11.5 0.0 SER A 59 0 13.5 3.5 7.0 3.0 0.0 PRO A 60 0 11.5 6.0 1.5 4.0 0.0 ASP A 61 1 12.5 5.0 6.5 1.0 0.0 GLN A 62 7 24.0 4.0 19.0 1.0 0.0 VAL A 63 4 19.5 5.5 14.0 0.0 0.0 GLY A 64 0 14.5 4.5 4.5 5.5 0.0 VAL A 65 5 24.5 5.0 12.0 7.5 0.0 LYS A 66 18 16.5 7.5 9.0 0.0 0.0 MET A 67 5 19.0 6.0 9.0 4.0 0.0 GLY A 68 0 7.0 4.0 2.5 0.5 0.0 TRP A 69 7 25.0 5.0 0.0 20.0 0.0 LYS A 70 6 23.5 7.0 4.0 12.5 0.0 SER A 71 0 20.0 7.5 0.5 12.0 0.0 LYS A 72 10 14.5 7.5 3.5 3.5 0.0 ALA A 73 1 20.0 7.5 1.5 11.0 0.0 GLY A 74 0 10.5 4.5 1.0 5.0 0.0 ASP A 75 3 19.5 4.5 4.0 11.0 0.0 THR A 76 2 21.0 8.0 1.5 11.5 0.0 ILE A 77 7 26.5 9.0 0.5 17.0 0.0 VAL A 78 4 14.5 8.0 2.0 4.5 0.0 CYS A 79 1 15.5 6.0 2.5 7.0 0.0 LEU A 80 12 15.0 10.0 5.0 0.0 0.0 PRO A 81 0 21.0 12.5 2.0 6.5 0.0 HIS A 82 3 26.5 8.0 6.5 12.0 0.0 LYS A 83 10 18.5 5.0 3.0 10.5 0.0 VAL A 84 5 26.5 6.5 5.0 15.0 0.0 PHE A 85 5 23.5 7.0 4.0 12.5 0.0 VAL A 86 5 28.0 5.5 0.5 22.0 0.0 GLU A 87 3 21.0 7.0 4.0 10.0 0.0 ILE A 88 11 50.0 10.0 1.0 39.0 0.0 LYS A 89 11 27.5 11.0 0.0 16.5 0.0 SER A 90 3 19.5 8.0 2.5 9.0 0.0 THR A 91 2 17.0 4.5 0.0 12.5 0.0 GLN A 92 5 7.0 4.5 2.0 0.5 0.0 LYS A 93 12 7.5 7.5 0.0 0.0 0.0 ASP A 94 1 7.5 7.5 0.0 0.0 0.0 SER A 95 0 7.0 7.0 0.0 0.0 0.0 LYS A 96 9 9.0 9.0 0.0 0.0 0.0 ASP A 97 3 10.0 9.5 0.5 0.0 0.0 PRO A 98 0 7.0 7.0 0.0 0.0 0.0 ASP A 99 1 5.5 5.0 0.5 0.0 0.0 THR A 100 2 4.0 4.0 0.0 0.0 0.0 ASP A 101 1 4.0 4.0 0.0 0.0 0.0 LEU A 102 4 7.0 6.5 0.5 0.0 0.0 ILE A 103 10 5.5 5.5 0.0 0.0 0.0 VAL A 104 2 4.5 3.5 1.0 0.0 0.0 PRO A 105 0 4.0 4.0 0.0 0.0 0.0 ASN A 106 3 5.0 4.5 0.5 0.0 0.0 LEU A 107 8 6.5 6.5 0.0 0.0 0.0 GLU A 108 3 4.0 4.0 0.0 0.0 0.0 HIS A 109 0 0.0 0.0 0.0 0.0 0.0 HIS A 110 0 0.0 0.0 0.0 0.0 0.0 HIS A 111 0 0.0 0.0 0.0 0.0 0.0 HIS A 112 0 0.0 0.0 0.0 0.0 0.0 HIS A 113 0 0.0 0.0 0.0 0.0 0.0 HIS A 114 0 0.0 0.0 0.0 0.0 0.0 TOTAL 485 2057.0 722.0 314.0 1021.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_