Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.9 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2013 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.9-exp mar may 14 00:20:00 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 ...) 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 `SOR77_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 19 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 18 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 80 MET ALA ILE GLN SER LYS TYR SER ASN THR GLN VAL GLU > ReadCoordsPdb(): Counting models in file `SOR77_R3Cons_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): I'm reading file SOR77_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2526 ATOM records read from file > ReadCoordsPdb(): --> 2526 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2526 (782 C, 1272 H, 234 O, 232 N, 6 S, 0 Q, 0 Metals) > INFO_mol: # residues: 160 (Avg. mol. weight: 111.6) > INFO_mol: # -- M.W. : 17860.1 g/mol. (17.86 kD) Estimated RoG : 15.14 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SOR77_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 160 > INFO_mol: Radius of Gyration : 16.7866 angstroms > INFO_mol: Center of Masses: x_cm(0.142), y_cm(0.130), z_cm(0.233) > INFO_res: MAIQSKYSNT QVESLIAEIL VVLEKHKAPT DLSLMALGNC VTHLLERKVP > INFO_res: SESRQAVAEQ FAKALAQSVK SNLEHHHHHH MAIQSKYSNT QVESLIAEIL > INFO_res: VVLEKHKAPT DLSLMALGNC VTHLLERKVP SESRQAVAEQ FAKALAQSVK > INFO_res: SNLEHHHHHH > INFO_res: > INFO_res: MET ALA ILE GLN SER LYS TYR SER ASN THR GLN VAL > INFO_res: GLU SER LEU ILE ALA GLU ILE LEU VAL VAL LEU GLU > INFO_res: LYS HIS LYS ALA PRO THR ASP LEU SER LEU MET ALA > INFO_res: LEU GLY ASN CYS VAL THR HIS LEU LEU GLU ARG LYS > INFO_res: VAL PRO SER GLU SER ARG GLN ALA VAL ALA GLU GLN > INFO_res: PHE ALA LYS ALA LEU ALA GLN SER VAL LYS SER ASN > INFO_res: LEU GLU HIS HIS HIS HIS HIS HIS MET ALA ILE GLN > INFO_res: SER LYS TYR SER ASN THR GLN VAL GLU SER LEU ILE > INFO_res: ALA GLU ILE LEU VAL VAL LEU GLU LYS HIS LYS ALA > INFO_res: PRO THR ASP LEU SER LEU MET ALA LEU GLY ASN CYS > INFO_res: VAL THR HIS LEU LEU GLU ARG LYS VAL PRO SER GLU > INFO_res: SER ARG GLN ALA VAL ALA GLU GLN PHE ALA LYS ALA > INFO_res: LEU ALA GLN SER VAL LYS SER ASN LEU GLU HIS HIS > INFO_res: HIS HIS HIS HIS > INFO_res: > INFO_res: 18 ALA 4 ARG 6 ASN 2 ASP 2 CYS 10 GLN > INFO_res: 14 GLU 2 GLY 16 HIS 6 ILE 20 LEU 12 LYS > INFO_res: 4 MET 2 PHE 4 PRO 16 SER 6 THR 2 TYR > INFO_res: 14 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `SOR77_R3Cons_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1356 NOE-distance constraints (0 Ambiguous NOE/s) read 1356 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1356 INTRA-RESIDUE RESTRAINTS (I=J) : 0 SEQUENTIAL RESTRAINTS (I-J)=1 : 198 BACKBONE-BACKBONE : 98 BACKBONE-SIDE CHAIN : 64 SIDE CHAIN-SIDE CHAIN : 36 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 778 BACKBONE-BACKBONE : 304 BACKBONE-SIDE CHAIN : 174 SIDE CHAIN-SIDE CHAIN : 300 LONG RANGE RESTRAINTS (I-J)>=5 : 380 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1048 INTER-CHAIN RESTRAINTS : 308 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 ILE A 3 0 0.0 0.0 0.0 0.0 0.0 GLN A 4 0 0.0 0.0 0.0 0.0 0.0 SER A 5 0 1.0 0.0 1.0 0.0 0.0 LYS A 6 0 2.0 2.0 0.0 0.0 0.0 TYR A 7 0 12.5 2.0 2.0 8.5 6.5 SER A 8 0 4.0 0.5 3.5 0.0 0.0 ASN A 9 0 4.5 1.0 3.5 0.0 0.0 THR A 10 0 4.5 1.5 3.0 0.0 0.0 GLN A 11 0 10.5 1.5 6.0 3.0 3.0 VAL A 12 0 15.5 1.0 9.0 5.5 3.5 GLU A 13 0 7.5 1.0 6.5 0.0 0.0 SER A 14 0 5.5 1.0 4.5 0.0 0.0 LEU A 15 0 15.5 2.0 7.5 6.0 6.0 ILE A 16 0 18.5 1.5 9.5 7.5 7.5 ALA A 17 0 6.0 1.0 5.0 0.0 0.0 GLU A 18 0 9.5 2.0 7.5 0.0 2.5 ILE A 19 0 13.5 1.5 10.0 2.0 6.0 LEU A 20 0 11.5 1.5 5.5 4.5 4.5 VAL A 21 0 10.0 2.0 8.0 0.0 0.0 VAL A 22 0 13.5 2.0 11.0 0.5 4.0 LEU A 23 0 16.5 1.5 6.5 8.5 3.0 GLU A 24 0 6.0 1.0 5.0 0.0 0.0 LYS A 25 0 10.0 1.5 8.5 0.0 0.0 HIS A 26 0 10.0 1.5 6.0 2.5 2.5 LYS A 27 0 3.5 1.5 2.0 0.0 0.0 ALA A 28 0 14.0 2.5 5.0 6.5 1.5 PRO A 29 0 7.5 2.5 4.5 0.5 0.5 THR A 30 0 7.5 1.0 3.5 3.0 3.0 ASP A 31 0 5.0 0.5 4.0 0.5 0.5 LEU A 32 0 20.5 1.0 11.0 8.5 8.5 SER A 33 0 11.0 1.5 4.0 5.5 2.0 LEU A 34 0 14.5 1.5 8.5 4.5 4.5 MET A 35 0 11.0 1.0 7.5 2.5 2.5 ALA A 36 0 13.0 0.5 5.5 7.0 6.0 LEU A 37 0 12.5 0.5 10.0 2.0 3.5 GLY A 38 0 11.0 1.5 5.5 4.0 4.5 ASN A 39 0 12.0 2.0 7.5 2.5 2.5 CYS A 40 0 11.5 2.5 7.0 2.0 3.0 VAL A 41 0 25.0 3.0 12.5 9.5 8.0 THR A 42 0 13.0 1.5 6.0 5.5 5.5 HIS A 43 0 10.0 2.0 4.5 3.5 3.5 LEU A 44 0 10.5 2.5 4.0 4.0 4.0 LEU A 45 0 16.0 1.0 8.0 7.0 0.5 GLU A 46 0 6.5 1.0 2.5 3.0 0.0 ARG A 47 0 3.0 1.0 2.0 0.0 0.0 LYS A 48 0 4.5 2.0 1.0 1.5 1.5 VAL A 49 0 13.0 3.5 5.0 4.5 0.0 PRO A 50 0 6.5 2.5 4.0 0.0 0.0 SER A 51 0 8.0 1.0 6.5 0.5 0.5 GLU A 52 0 4.0 1.0 3.0 0.0 0.0 SER A 53 0 10.5 1.5 9.0 0.0 0.0 ARG A 54 0 24.5 1.5 9.0 14.0 4.0 GLN A 55 0 7.5 1.5 3.0 3.0 3.0 ALA A 56 0 8.5 2.0 6.5 0.0 0.0 VAL A 57 0 13.5 2.0 8.0 3.5 1.0 ALA A 58 0 12.0 2.0 6.0 4.0 2.5 GLU A 59 0 8.0 1.5 6.5 0.0 0.0 GLN A 60 0 8.5 1.0 7.5 0.0 0.0 PHE A 61 0 18.0 1.5 8.0 8.5 6.5 ALA A 62 0 11.5 1.5 10.0 0.0 1.0 LYS A 63 0 6.0 1.5 4.5 0.0 0.0 ALA A 64 0 6.0 1.5 4.5 0.0 0.0 LEU A 65 0 19.5 1.0 9.0 9.5 9.5 ALA A 66 0 6.5 0.5 5.5 0.5 1.0 GLN A 67 0 3.5 0.0 3.5 0.0 0.0 SER A 68 0 5.0 1.5 3.0 0.5 0.5 VAL A 69 0 15.5 2.0 4.5 9.0 9.0 LYS A 70 0 5.0 0.5 4.0 0.5 0.5 SER A 71 0 1.5 0.5 1.0 0.0 0.0 ASN A 72 0 2.0 1.0 1.0 0.0 0.0 LEU A 73 0 2.0 0.5 1.0 0.5 0.5 GLU A 74 0 0.5 0.0 0.5 0.0 0.0 HIS A 75 0 0.0 0.0 0.0 0.0 0.0 HIS A 76 0 0.0 0.0 0.0 0.0 0.0 HIS A 77 0 0.0 0.0 0.0 0.0 0.0 HIS A 78 0 0.0 0.0 0.0 0.0 0.0 HIS A 79 0 0.0 0.0 0.0 0.0 0.0 HIS A 80 0 0.0 0.0 0.0 0.0 0.0 MET B 1 0 0.0 0.0 0.0 0.0 0.0 ALA B 2 0 0.0 0.0 0.0 0.0 0.0 ILE B 3 0 0.0 0.0 0.0 0.0 0.0 GLN B 4 0 0.0 0.0 0.0 0.0 0.0 SER B 5 0 1.0 0.0 1.0 0.0 0.0 LYS B 6 0 2.0 2.0 0.0 0.0 0.0 TYR B 7 0 12.5 2.0 2.0 8.5 6.5 SER B 8 0 4.0 0.5 3.5 0.0 0.0 ASN B 9 0 4.5 1.0 3.5 0.0 0.0 THR B 10 0 4.5 1.5 3.0 0.0 0.0 GLN B 11 0 10.5 1.5 6.0 3.0 3.0 VAL B 12 0 15.5 1.0 9.0 5.5 3.5 GLU B 13 0 7.5 1.0 6.5 0.0 0.0 SER B 14 0 5.5 1.0 4.5 0.0 0.0 LEU B 15 0 15.5 2.0 7.5 6.0 6.0 ILE B 16 0 18.5 1.5 9.5 7.5 7.5 ALA B 17 0 6.0 1.0 5.0 0.0 0.0 GLU B 18 0 9.5 2.0 7.5 0.0 2.5 ILE B 19 0 13.5 1.5 10.0 2.0 6.0 LEU B 20 0 11.5 1.5 5.5 4.5 4.5 VAL B 21 0 10.0 2.0 8.0 0.0 0.0 VAL B 22 0 13.5 2.0 11.0 0.5 4.0 LEU B 23 0 16.5 1.5 6.5 8.5 3.0 GLU B 24 0 6.0 1.0 5.0 0.0 0.0 LYS B 25 0 10.0 1.5 8.5 0.0 0.0 HIS B 26 0 10.0 1.5 6.0 2.5 2.5 LYS B 27 0 3.5 1.5 2.0 0.0 0.0 ALA B 28 0 14.0 2.5 5.0 6.5 1.5 PRO B 29 0 7.5 2.5 4.5 0.5 0.5 THR B 30 0 7.5 1.0 3.5 3.0 3.0 ASP B 31 0 5.0 0.5 4.0 0.5 0.5 LEU B 32 0 20.5 1.0 11.0 8.5 8.5 SER B 33 0 11.0 1.5 4.0 5.5 2.0 LEU B 34 0 14.5 1.5 8.5 4.5 4.5 MET B 35 0 11.0 1.0 7.5 2.5 2.5 ALA B 36 0 13.0 0.5 5.5 7.0 6.0 LEU B 37 0 12.5 0.5 10.0 2.0 3.5 GLY B 38 0 11.0 1.5 5.5 4.0 4.5 ASN B 39 0 12.0 2.0 7.5 2.5 2.5 CYS B 40 0 11.5 2.5 7.0 2.0 3.0 VAL B 41 0 25.0 3.0 12.5 9.5 8.0 THR B 42 0 13.0 1.5 6.0 5.5 5.5 HIS B 43 0 10.0 2.0 4.5 3.5 3.5 LEU B 44 0 10.5 2.5 4.0 4.0 4.0 LEU B 45 0 16.0 1.0 8.0 7.0 0.5 GLU B 46 0 6.5 1.0 2.5 3.0 0.0 ARG B 47 0 3.0 1.0 2.0 0.0 0.0 LYS B 48 0 4.5 2.0 1.0 1.5 1.5 VAL B 49 0 13.0 3.5 5.0 4.5 0.0 PRO B 50 0 6.5 2.5 4.0 0.0 0.0 SER B 51 0 8.0 1.0 6.5 0.5 0.5 GLU B 52 0 4.0 1.0 3.0 0.0 0.0 SER B 53 0 10.5 1.5 9.0 0.0 0.0 ARG B 54 0 24.5 1.5 9.0 14.0 4.0 GLN B 55 0 7.5 1.5 3.0 3.0 3.0 ALA B 56 0 8.5 2.0 6.5 0.0 0.0 VAL B 57 0 13.5 2.0 8.0 3.5 1.0 ALA B 58 0 12.0 2.0 6.0 4.0 2.5 GLU B 59 0 8.0 1.5 6.5 0.0 0.0 GLN B 60 0 8.5 1.0 7.5 0.0 0.0 PHE B 61 0 18.0 1.5 8.0 8.5 6.5 ALA B 62 0 11.5 1.5 10.0 0.0 1.0 LYS B 63 0 6.0 1.5 4.5 0.0 0.0 ALA B 64 0 6.0 1.5 4.5 0.0 0.0 LEU B 65 0 19.5 1.0 9.0 9.5 9.5 ALA B 66 0 6.5 0.5 5.5 0.5 1.0 GLN B 67 0 3.5 0.0 3.5 0.0 0.0 SER B 68 0 5.0 1.5 3.0 0.5 0.5 VAL B 69 0 15.5 2.0 4.5 9.0 9.0 LYS B 70 0 5.0 0.5 4.0 0.5 0.5 SER B 71 0 1.5 0.5 1.0 0.0 0.0 ASN B 72 0 2.0 1.0 1.0 0.0 0.0 LEU B 73 0 2.0 0.5 1.0 0.5 0.5 GLU B 74 0 0.5 0.0 0.5 0.0 0.0 HIS B 75 0 0.0 0.0 0.0 0.0 0.0 HIS B 76 0 0.0 0.0 0.0 0.0 0.0 HIS B 77 0 0.0 0.0 0.0 0.0 0.0 HIS B 78 0 0.0 0.0 0.0 0.0 0.0 HIS B 79 0 0.0 0.0 0.0 0.0 0.0 HIS B 80 0 0.0 0.0 0.0 0.0 0.0 TOTAL 0 1356.0 198.0 778.0 380.0 308.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_