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 `GMR137_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 78 MET ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL ASP 1 > ReadCoordsPdb(): Counting models in file `GMR137_R3_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 GMR137_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1174 ATOM records read from file > ReadCoordsPdb(): --> 1174 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1174 (375 C, 574 H, 121 O, 102 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 78 (Avg. mol. weight: 109.1) > INFO_mol: # -- M.W. : 8511.3 g/mol. (8.51 kD) Estimated RoG : 11.52 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `GMR137_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 78 > INFO_mol: Radius of Gyration : 12.0646 angstroms > INFO_mol: Center of Masses: x_cm(-2.647), y_cm(-0.285), z_cm(-1.016) > INFO_res: MNLTVNGKPS TVDGAESLNV TELLSALKVA QAEYVTVELN GEVLEREAFD > INFO_res: ATTVKDGDAV EFLYFMGGGK LEHHHHHH > INFO_res: > INFO_res: MET ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL > INFO_res: ASP GLY ALA GLU SER LEU ASN VAL THR GLU LEU LEU > INFO_res: SER ALA LEU LYS VAL ALA GLN ALA GLU TYR VAL THR > INFO_res: VAL GLU LEU ASN GLY GLU VAL LEU GLU ARG GLU ALA > INFO_res: PHE ASP ALA THR THR VAL LYS ASP GLY ASP ALA VAL > INFO_res: GLU PHE LEU TYR PHE MET GLY GLY GLY LYS LEU GLU > INFO_res: HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 7 ALA 1 ARG 4 ASN 4 ASP 1 GLN 9 GLU > INFO_res: 7 GLY 6 HIS 9 LEU 4 LYS 2 MET 3 PHE > INFO_res: 1 PRO 3 SER 6 THR 2 TYR 9 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `GMR137_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 979 NOE-distance constraints (0 Ambiguous NOE/s) read 979 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 979 INTRA-RESIDUE RESTRAINTS (I=J) : 144 SEQUENTIAL RESTRAINTS (I-J)=1 : 359 BACKBONE-BACKBONE : 93 BACKBONE-SIDE CHAIN : 57 SIDE CHAIN-SIDE CHAIN : 209 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 207 BACKBONE-BACKBONE : 52 BACKBONE-SIDE CHAIN : 33 SIDE CHAIN-SIDE CHAIN : 122 LONG RANGE RESTRAINTS (I-J)>=5 : 269 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 979 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 0 18.5 3.0 4.0 11.5 0.0 ASN A 2 4 11.0 5.5 0.0 5.5 0.0 LEU A 3 5 24.5 5.5 4.5 14.5 0.0 THR A 4 2 14.0 4.5 4.0 5.5 0.0 VAL A 5 0 9.5 3.5 2.5 3.5 0.0 ASN A 6 3 13.0 3.5 3.0 6.5 0.0 GLY A 7 0 5.0 2.0 2.0 1.0 0.0 LYS A 8 3 13.0 7.0 6.0 0.0 0.0 PRO A 9 0 9.0 8.5 0.0 0.5 0.0 SER A 10 1 8.5 3.5 0.0 5.0 0.0 THR A 11 2 10.0 5.5 1.0 3.5 0.0 VAL A 12 1 15.0 7.5 1.0 6.5 0.0 ASP A 13 2 7.5 6.0 1.5 0.0 0.0 GLY A 14 0 3.0 3.0 0.0 0.0 0.0 ALA A 15 0 6.5 2.5 3.5 0.5 0.0 GLU A 16 0 4.0 4.0 0.0 0.0 0.0 SER A 17 0 7.0 5.5 1.0 0.5 0.0 LEU A 18 4 19.0 6.5 5.0 7.5 0.0 ASN A 19 6 20.0 5.5 7.0 7.5 0.0 VAL A 20 2 28.0 5.0 6.0 17.0 0.0 THR A 21 2 16.5 6.0 6.5 4.0 0.0 GLU A 22 4 16.0 5.5 10.5 0.0 0.0 LEU A 23 5 17.0 4.0 6.0 7.0 0.0 LEU A 24 5 19.5 6.0 7.0 6.5 0.0 SER A 25 1 11.5 6.5 5.0 0.0 0.0 ALA A 26 0 8.5 4.0 4.0 0.5 0.0 LEU A 27 8 7.5 3.5 3.5 0.5 0.0 LYS A 28 1 7.0 4.5 2.5 0.0 0.0 VAL A 29 3 15.5 7.0 4.0 4.5 0.0 ALA A 30 0 9.0 9.0 0.0 0.0 0.0 GLN A 31 2 17.0 8.0 9.0 0.0 0.0 ALA A 32 0 11.0 4.5 4.5 2.0 0.0 GLU A 33 2 6.5 6.0 0.5 0.0 0.0 TYR A 34 4 17.0 7.5 9.5 0.0 0.0 VAL A 35 0 14.5 5.0 4.0 5.5 0.0 THR A 36 1 10.5 6.0 0.0 4.5 0.0 VAL A 37 2 13.5 5.5 3.0 5.0 0.0 GLU A 38 2 18.0 4.5 5.0 8.5 0.0 LEU A 39 5 13.5 8.0 3.0 2.5 0.0 ASN A 40 4 14.0 7.0 1.0 6.0 0.0 GLY A 41 0 5.5 2.0 3.0 0.5 0.0 GLU A 42 4 9.5 4.0 5.5 0.0 0.0 VAL A 43 3 15.0 6.5 0.5 8.0 0.0 LEU A 44 2 19.0 5.0 1.5 12.5 0.0 GLU A 45 3 12.5 5.0 7.5 0.0 0.0 ARG A 46 3 8.5 6.0 2.5 0.0 0.0 GLU A 47 3 10.0 6.0 4.0 0.0 0.0 ALA A 48 0 14.5 6.0 8.5 0.0 0.0 PHE A 49 4 31.5 5.5 6.0 20.0 0.0 ASP A 50 1 8.5 5.0 1.0 2.5 0.0 ALA A 51 0 7.0 4.5 2.5 0.0 0.0 THR A 52 2 13.0 4.0 2.5 6.5 0.0 THR A 53 2 10.5 5.0 0.0 5.5 0.0 VAL A 54 2 17.0 6.5 2.0 8.5 0.0 LYS A 55 4 11.0 8.0 1.5 1.5 0.0 ASP A 56 2 16.0 7.0 0.5 8.5 0.0 GLY A 57 0 7.5 4.0 0.0 3.5 0.0 ASP A 58 0 13.5 4.0 3.5 6.0 0.0 ALA A 59 0 13.0 3.5 0.0 9.5 0.0 VAL A 60 2 9.0 3.0 3.0 3.0 0.0 GLU A 61 0 10.5 4.5 2.0 4.0 0.0 PHE A 62 4 19.0 5.5 3.0 10.5 0.0 LEU A 63 4 13.0 7.5 3.5 2.0 0.0 TYR A 64 4 6.5 6.5 0.0 0.0 0.0 PHE A 65 2 9.0 4.5 1.5 3.0 0.0 MET A 66 2 4.5 4.5 0.0 0.0 0.0 GLY A 67 0 2.5 2.5 0.0 0.0 0.0 GLY A 68 0 1.0 0.5 0.5 0.0 0.0 GLY A 69 0 0.0 0.0 0.0 0.0 0.0 LYS A 70 2 2.5 2.0 0.5 0.0 0.0 LEU A 71 3 3.0 3.0 0.0 0.0 0.0 GLU A 72 0 1.0 1.0 0.0 0.0 0.0 HIS A 73 0 0.5 0.5 0.0 0.0 0.0 HIS A 74 0 0.5 0.5 0.0 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 TOTAL 144 835.0 359.0 207.0 269.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_