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 `ZR18_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 19-JUN-03 1PQX > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF STAPHYLOCOCCUS AUREUS PROTEIN > ReadCoordsPdb(): >> TITLE 2 SAV1430. NORTHEAST STRUCUTRAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 ZR18. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): Counting models in file `ZR18_NMR_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 10 model(s) > ReadCoordsPdb(): what model do you want [(1 to 10) or all] ?_ > ReadCoordsPdb(): I'm reading file ZR18_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1444 ATOM records read from file > ReadCoordsPdb(): --> 1444 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1444 (462 C, 708 H, 146 O, 124 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 91 (Avg. mol. weight: 115.0) > INFO_mol: # -- M.W. : 10463.5 g/mol. (10.46 kD) Estimated RoG : 12.21 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `ZR18_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 91 > INFO_mol: Radius of Gyration : 13.9331 angstroms > INFO_mol: Center of Masses: x_cm(2.656), y_cm(0.664), z_cm(-0.826) > INFO_res: MKIISISETP NHNTMKITLS ESREGMTSDT YTKVDDSQPA FINDILKVEG > INFO_res: VKSIFHVMDF ISVDKENDAN WETVLPKVEA VFELEHHHHH H > INFO_res: > INFO_res: MET LYS ILE ILE SER ILE SER GLU THR PRO ASN HIS > INFO_res: ASN THR MET LYS ILE THR LEU SER GLU SER ARG GLU > INFO_res: GLY MET THR SER ASP THR TYR THR LYS VAL ASP ASP > INFO_res: SER GLN PRO ALA PHE ILE ASN ASP ILE LEU LYS VAL > INFO_res: GLU GLY VAL LYS SER ILE PHE HIS VAL MET ASP PHE > INFO_res: ILE SER VAL ASP LYS GLU ASN ASP ALA ASN TRP GLU > INFO_res: THR VAL LEU PRO LYS VAL GLU ALA VAL PHE GLU LEU > INFO_res: GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 3 ALA 1 ARG 5 ASN 7 ASP 1 GLN 9 GLU > INFO_res: 2 GLY 8 HIS 8 ILE 4 LEU 7 LYS 4 MET > INFO_res: 4 PHE 3 PRO 8 SER 7 THR 1 TYR 1 TRP > INFO_res: 8 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `ZR18_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1137 NOE-distance constraints (0 Ambiguous NOE/s) read 1137 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1137 INTRA-RESIDUE RESTRAINTS (I=J) : 168 SEQUENTIAL RESTRAINTS (I-J)=1 : 337 BACKBONE-BACKBONE : 82 BACKBONE-SIDE CHAIN : 37 SIDE CHAIN-SIDE CHAIN : 218 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 217 BACKBONE-BACKBONE : 30 BACKBONE-SIDE CHAIN : 43 SIDE CHAIN-SIDE CHAIN : 144 LONG RANGE RESTRAINTS (I-J)>=5 : 415 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1137 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 0 4.5 1.0 0.0 3.5 0.0 LYS A 2 4 4.5 2.0 0.5 2.0 0.0 ILE A 3 4 17.5 4.5 2.0 11.0 0.0 ILE A 4 4 16.0 7.0 0.5 8.5 0.0 SER A 5 0 8.0 4.0 1.0 3.0 0.0 ILE A 6 5 8.0 3.0 1.5 3.5 0.0 SER A 7 0 6.5 4.0 0.0 2.5 0.0 GLU A 8 3 4.5 4.0 0.5 0.0 0.0 THR A 9 0 6.0 5.0 1.0 0.0 0.0 PRO A 10 0 5.5 5.5 0.0 0.0 0.0 ASN A 11 2 4.0 3.0 1.0 0.0 0.0 HIS A 12 1 1.5 0.0 0.5 1.0 0.0 ASN A 13 2 5.0 1.0 0.0 4.0 0.0 THR A 14 0 9.5 2.5 0.5 6.5 0.0 MET A 15 0 16.0 4.0 0.0 12.0 0.0 LYS A 16 6 12.5 3.5 0.0 9.0 0.0 ILE A 17 4 15.0 3.5 0.5 11.0 0.0 THR A 18 1 13.5 5.0 0.0 8.5 0.0 LEU A 19 3 17.5 5.0 2.5 10.0 0.0 SER A 20 0 8.5 3.5 0.0 5.0 0.0 GLU A 21 1 6.0 3.0 2.0 1.0 0.0 SER A 22 1 4.0 3.0 0.0 1.0 0.0 ARG A 23 3 4.0 3.5 0.5 0.0 0.0 GLU A 24 1 4.5 4.5 0.0 0.0 0.0 GLY A 25 0 3.5 2.5 1.0 0.0 0.0 MET A 26 1 5.0 1.5 0.0 3.5 0.0 THR A 27 0 3.0 2.5 0.5 0.0 0.0 SER A 28 0 7.5 3.0 0.0 4.5 0.0 ASP A 29 0 9.0 3.0 1.5 4.5 0.0 THR A 30 1 6.0 3.0 0.0 3.0 0.0 TYR A 31 2 22.5 3.5 3.5 15.5 0.0 THR A 32 0 6.5 4.0 0.0 2.5 0.0 LYS A 33 4 4.5 3.0 0.5 1.0 0.0 VAL A 34 3 15.5 3.0 2.0 10.5 0.0 ASP A 35 0 6.5 2.5 3.0 1.0 0.0 ASP A 36 0 1.5 1.0 0.0 0.5 0.0 SER A 37 0 3.0 2.5 0.5 0.0 0.0 GLN A 38 6 17.0 5.0 6.5 5.5 0.0 PRO A 39 0 19.5 5.0 13.0 1.5 0.0 ALA A 40 0 7.0 3.5 3.5 0.0 0.0 PHE A 41 1 10.5 3.0 3.5 4.0 0.0 ILE A 42 6 36.0 5.5 20.0 10.5 0.0 ASN A 43 7 18.0 5.0 6.0 7.0 0.0 ASP A 44 0 7.0 2.0 3.5 1.5 0.0 ILE A 45 6 21.5 4.5 6.5 10.5 0.0 LEU A 46 3 24.5 5.0 4.5 15.0 0.0 LYS A 47 7 11.0 4.0 4.0 3.0 0.0 VAL A 48 2 19.5 7.0 5.0 7.5 0.0 GLU A 49 1 7.0 6.5 0.5 0.0 0.0 GLY A 50 0 8.0 3.0 0.5 4.5 0.0 VAL A 51 2 13.5 3.0 3.5 7.0 0.0 LYS A 52 5 7.5 3.5 0.0 4.0 0.0 SER A 53 0 9.0 3.5 0.5 5.0 0.0 ILE A 54 4 27.5 5.0 1.5 21.0 0.0 PHE A 55 1 15.5 5.0 3.0 7.5 0.0 HIS A 56 2 17.5 4.5 2.0 11.0 0.0 VAL A 57 2 18.0 6.0 7.5 4.5 0.0 MET A 58 1 6.5 5.0 1.5 0.0 0.0 ASP A 59 0 7.0 3.5 0.0 3.5 0.0 PHE A 60 1 21.5 6.0 7.0 8.5 0.0 ILE A 61 5 25.5 6.5 2.0 17.0 0.0 SER A 62 0 12.0 4.5 1.5 6.0 0.0 VAL A 63 2 17.0 3.5 1.0 12.5 0.0 ASP A 64 0 12.0 3.0 0.0 9.0 0.0 LYS A 65 10 19.0 5.0 2.5 11.5 0.0 GLU A 66 2 13.5 5.5 4.0 4.0 0.0 ASN A 67 0 5.0 3.0 0.0 2.0 0.0 ASP A 68 0 3.0 2.0 1.0 0.0 0.0 ALA A 69 0 9.0 1.5 5.5 2.0 0.0 ASN A 70 1 4.5 2.0 2.5 0.0 0.0 TRP A 71 5 30.0 2.5 7.5 20.0 0.0 GLU A 72 1 5.5 3.0 2.5 0.0 0.0 THR A 73 0 9.5 6.0 3.5 0.0 0.0 VAL A 74 3 18.5 6.0 9.0 3.5 0.0 LEU A 75 4 15.0 5.5 8.5 1.0 0.0 PRO A 76 0 8.0 6.5 1.5 0.0 0.0 LYS A 77 9 19.0 6.0 6.5 6.5 0.0 VAL A 78 3 16.5 5.5 7.5 3.5 0.0 GLU A 79 1 10.0 4.0 4.5 1.5 0.0 ALA A 80 0 6.5 3.0 3.5 0.0 0.0 VAL A 81 3 16.0 4.5 4.0 7.5 0.0 PHE A 82 2 20.5 5.0 3.0 12.5 0.0 GLU A 83 1 10.5 6.0 3.5 1.0 0.0 LEU A 84 2 10.0 6.5 1.5 2.0 0.0 GLU A 85 1 3.5 3.5 0.0 0.0 0.0 HIS A 86 0 2.0 2.0 0.0 0.0 0.0 HIS A 87 0 1.0 1.0 0.0 0.0 0.0 HIS A 88 0 0.0 0.0 0.0 0.0 0.0 HIS A 89 0 0.0 0.0 0.0 0.0 0.0 HIS A 90 0 0.0 0.0 0.0 0.0 0.0 HIS A 91 0 0.0 0.0 0.0 0.0 0.0 TOTAL 168 969.0 337.0 217.0 415.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_