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 `HR4694F_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER TRANSFERASE 30-JUN-10 2L05 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE RAS-BINDING DOMAIN OF SERINE/THREONINE- > ReadCoordsPdb(): >> TITLE 2 PROTEIN KINASE B-RAF FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET HR4694F > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `HR4694F_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 HR4694F_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1398 ATOM records read from file > ReadCoordsPdb(): --> 1398 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1398 (435 C, 715 H, 120 O, 122 N, 6 S, 0 Q, 0 Metals) > INFO_mol: # residues: 86 (Avg. mol. weight: 113.6) > INFO_mol: # -- M.W. : 9766.4 g/mol. (9.77 kD) Estimated RoG : 11.95 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `HR4694F_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 86 > INFO_mol: Radius of Gyration : 13.8796 angstroms > INFO_mol: Center of Masses: x_cm(-0.068), y_cm(1.601), z_cm(0.681) > INFO_res: HMPKSPQKPI VRVFLPNKQR TVVPARCGVT VRDSLKKALM MRGLIPECCA > INFO_res: VYRIQDGEKK PIGWDTDISW LTGEELHVEV LENVPL > INFO_res: > INFO_res: HIS MET PRO LYS SER PRO GLN LYS PRO ILE VAL ARG > INFO_res: VAL PHE LEU PRO ASN LYS GLN ARG THR VAL VAL PRO > INFO_res: ALA ARG CYS GLY VAL THR VAL ARG ASP SER LEU LYS > INFO_res: LYS ALA LEU MET MET ARG GLY LEU ILE PRO GLU CYS > INFO_res: CYS ALA VAL TYR ARG ILE GLN ASP GLY GLU LYS LYS > INFO_res: PRO ILE GLY TRP ASP THR ASP ILE SER TRP LEU THR > INFO_res: GLY GLU GLU LEU HIS VAL GLU VAL LEU GLU ASN VAL > INFO_res: PRO LEU > INFO_res: > INFO_res: 3 ALA 6 ARG 2 ASN 4 ASP 3 CYS 3 GLN > INFO_res: 6 GLU 5 GLY 2 HIS 5 ILE 8 LEU 7 LYS > INFO_res: 3 MET 1 PHE 8 PRO 3 SER 4 THR 1 TYR > INFO_res: 2 TRP 10 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `HR4694F_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1755 NOE-distance constraints (0 Ambiguous NOE/s) read 1755 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1755 INTRA-RESIDUE RESTRAINTS (I=J) : 455 SEQUENTIAL RESTRAINTS (I-J)=1 : 498 BACKBONE-BACKBONE : 108 BACKBONE-SIDE CHAIN : 104 SIDE CHAIN-SIDE CHAIN : 286 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 256 BACKBONE-BACKBONE : 56 BACKBONE-SIDE CHAIN : 55 SIDE CHAIN-SIDE CHAIN : 145 LONG RANGE RESTRAINTS (I-J)>=5 : 546 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1755 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain HIS A 1 0 0.0 0.0 0.0 0.0 0.0 MET A 2 4 2.5 2.5 0.0 0.0 0.0 PRO A 3 0 3.5 3.5 0.0 0.0 0.0 LYS A 4 12 3.0 3.0 0.0 0.0 0.0 SER A 5 1 3.5 3.5 0.0 0.0 0.0 PRO A 6 0 4.0 4.0 0.0 0.0 0.0 GLN A 7 6 5.5 5.5 0.0 0.0 0.0 LYS A 8 9 9.5 8.5 1.0 0.0 0.0 PRO A 9 0 15.0 7.5 0.0 7.5 0.0 ILE A 10 9 20.0 6.5 4.0 9.5 0.0 VAL A 11 5 24.0 7.0 0.0 17.0 0.0 ARG A 12 12 20.5 5.5 3.0 12.0 0.0 VAL A 13 5 19.0 5.5 1.5 12.0 0.0 PHE A 14 3 17.5 6.0 0.0 11.5 0.0 LEU A 15 7 26.5 7.5 9.5 9.5 0.0 PRO A 16 0 13.0 4.0 0.5 8.5 0.0 ASN A 17 6 4.0 2.5 1.5 0.0 0.0 LYS A 18 14 4.0 3.5 0.5 0.0 0.0 GLN A 19 11 13.5 4.0 9.5 0.0 0.0 ARG A 20 6 13.0 9.0 0.0 4.0 0.0 THR A 21 2 16.5 9.0 0.0 7.5 0.0 VAL A 22 5 14.5 6.5 0.0 8.0 0.0 VAL A 23 3 18.0 8.5 0.5 9.0 0.0 PRO A 24 0 11.5 8.0 0.0 3.5 0.0 ALA A 25 1 24.0 6.5 0.5 17.0 0.0 ARG A 26 12 19.5 9.0 6.0 4.5 0.0 CYS A 27 3 15.5 9.5 1.5 4.5 0.0 GLY A 28 0 7.0 6.0 0.0 1.0 0.0 VAL A 29 4 20.5 5.0 11.0 4.5 0.0 THR A 30 2 17.0 4.5 5.0 7.5 0.0 VAL A 31 5 24.0 4.0 4.5 15.5 0.0 ARG A 32 14 19.5 5.0 3.5 11.0 0.0 ASP A 33 3 16.0 4.5 11.5 0.0 0.0 SER A 34 3 19.5 5.0 6.0 8.5 0.0 LEU A 35 12 16.5 5.0 7.5 4.0 0.0 LYS A 36 20 13.0 4.0 9.0 0.0 0.0 LYS A 37 12 12.5 6.0 6.5 0.0 0.0 ALA A 38 1 16.5 6.0 8.0 2.5 0.0 LEU A 39 9 27.5 5.0 7.0 15.5 0.0 MET A 40 6 12.5 5.0 7.5 0.0 0.0 MET A 41 2 12.5 7.0 5.5 0.0 0.0 ARG A 42 12 17.5 8.0 8.0 1.5 0.0 GLY A 43 0 5.0 3.5 1.5 0.0 0.0 LEU A 44 10 17.5 4.0 4.5 9.0 0.0 ILE A 45 9 21.5 7.5 13.0 1.0 0.0 PRO A 46 0 19.0 8.5 2.5 8.0 0.0 GLU A 47 6 12.0 5.0 6.0 1.0 0.0 CYS A 48 3 12.0 2.0 9.0 1.0 0.0 CYS A 49 1 27.0 5.0 3.5 18.5 0.0 ALA A 50 1 16.5 6.5 1.5 8.5 0.0 VAL A 51 5 27.0 6.0 0.0 21.0 0.0 TYR A 52 3 31.0 6.0 4.5 20.5 0.0 ARG A 53 7 21.0 7.0 0.0 14.0 0.0 ILE A 54 9 25.5 8.0 6.5 11.0 0.0 GLN A 55 8 12.5 9.5 2.5 0.5 0.0 ASP A 56 0 11.0 8.5 2.5 0.0 0.0 GLY A 57 0 6.5 3.5 3.0 0.0 0.0 GLU A 58 9 10.5 6.0 4.5 0.0 0.0 LYS A 59 16 21.0 8.0 0.5 12.5 0.0 LYS A 60 13 16.0 9.5 0.5 6.0 0.0 PRO A 61 0 13.5 10.5 0.0 3.0 0.0 ILE A 62 7 24.5 6.0 2.0 16.5 0.0 GLY A 63 0 6.5 4.5 2.0 0.0 0.0 TRP A 64 9 37.5 3.5 1.5 32.5 0.0 ASP A 65 3 8.0 4.0 1.0 3.0 0.0 THR A 66 3 17.0 5.5 7.0 4.5 0.0 ASP A 67 2 13.0 5.5 4.0 3.5 0.0 ILE A 68 9 36.5 7.5 3.5 25.5 0.0 SER A 69 1 15.5 5.5 3.0 7.0 0.0 TRP A 70 7 12.5 4.5 8.0 0.0 0.0 LEU A 71 11 18.0 7.0 5.0 6.0 0.0 THR A 72 3 20.0 7.5 4.5 8.0 0.0 GLY A 73 0 9.0 5.5 0.0 3.5 0.0 GLU A 74 2 10.5 4.0 5.0 1.5 0.0 GLU A 75 4 19.0 8.0 0.0 11.0 0.0 LEU A 76 9 28.0 8.5 0.5 19.0 0.0 HIS A 77 2 15.5 5.0 0.0 10.5 0.0 VAL A 78 5 21.0 3.5 0.0 17.5 0.0 GLU A 79 3 13.5 5.5 0.0 8.0 0.0 VAL A 80 4 13.0 6.5 1.0 5.5 0.0 LEU A 81 10 15.0 4.5 0.0 10.5 0.0 GLU A 82 7 5.5 4.5 1.0 0.0 0.0 ASN A 83 4 6.5 6.0 0.5 0.0 0.0 VAL A 84 4 7.5 7.0 0.5 0.0 0.0 PRO A 85 0 6.0 6.0 0.0 0.0 0.0 LEU A 86 5 2.0 2.0 0.0 0.0 0.0 TOTAL 455 1300.0 498.0 256.0 546.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_