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 `RPR324_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 101 MET THR SER THR PHE ASP ARG VAL ALA THR ILE ILE ALA 1 > ReadCoordsPdb(): Counting models in file `RPR324_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 RPR324_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1575 ATOM records read from file > ReadCoordsPdb(): --> 1575 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1575 (505 C, 778 H, 155 O, 135 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 101 (Avg. mol. weight: 111.7) > INFO_mol: # -- M.W. : 11284.5 g/mol. (11.28 kD) Estimated RoG : 12.71 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `RPR324_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 101 > INFO_mol: Radius of Gyration : 14.6416 angstroms > INFO_mol: Center of Masses: x_cm(0.861), y_cm(0.840), z_cm(2.020) > INFO_res: MTSTFDRVAT IIAETCDIPR ETITPESHAI DDLGIDSLDF LDIAFAIDKA > INFO_res: FGIKLPLEKW TQEVNDGKAT TEQYFVLKNL AARIDELVAA KGALEHHHHH > INFO_res: H > INFO_res: > INFO_res: MET THR SER THR PHE ASP ARG VAL ALA THR ILE ILE > INFO_res: ALA GLU THR CYS ASP ILE PRO ARG GLU THR ILE THR > INFO_res: PRO GLU SER HIS ALA ILE ASP ASP LEU GLY ILE ASP > INFO_res: SER LEU ASP PHE LEU ASP ILE ALA PHE ALA ILE ASP > INFO_res: LYS ALA PHE GLY ILE LYS LEU PRO LEU GLU LYS TRP > INFO_res: THR GLN GLU VAL ASN ASP GLY LYS ALA THR THR GLU > INFO_res: GLN TYR PHE VAL LEU LYS ASN LEU ALA ALA ARG ILE > INFO_res: ASP GLU LEU VAL ALA ALA LYS GLY ALA LEU GLU HIS > INFO_res: HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 12 ALA 3 ARG 2 ASN 10 ASP 1 CYS 2 GLN > INFO_res: 8 GLU 4 GLY 7 HIS 10 ILE 9 LEU 6 LYS > INFO_res: 1 MET 5 PHE 3 PRO 3 SER 9 THR 1 TYR > INFO_res: 1 TRP 4 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `RPR324_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1792 NOE-distance constraints (0 Ambiguous NOE/s) read 1792 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1792 INTRA-RESIDUE RESTRAINTS (I=J) : 395 SEQUENTIAL RESTRAINTS (I-J)=1 : 431 BACKBONE-BACKBONE : 86 BACKBONE-SIDE CHAIN : 47 SIDE CHAIN-SIDE CHAIN : 298 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 486 BACKBONE-BACKBONE : 93 BACKBONE-SIDE CHAIN : 142 SIDE CHAIN-SIDE CHAIN : 251 LONG RANGE RESTRAINTS (I-J)>=5 : 480 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1792 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 THR A 2 1 3.5 0.0 1.5 2.0 0.0 SER A 3 0 2.5 2.0 0.5 0.0 0.0 THR A 4 2 14.5 3.5 3.0 8.0 0.0 PHE A 5 4 29.0 2.0 7.5 19.5 0.0 ASP A 6 0 7.0 2.0 3.0 2.0 0.0 ARG A 7 9 14.5 2.5 4.5 7.5 0.0 VAL A 8 5 25.5 4.5 8.0 13.0 0.0 ALA A 9 1 20.0 6.5 8.5 5.0 0.0 THR A 10 3 16.5 7.5 5.0 4.0 0.0 ILE A 11 10 21.5 7.0 5.5 9.0 0.0 ILE A 12 8 16.5 5.0 4.5 7.0 0.0 ALA A 13 1 15.5 5.0 3.5 7.0 0.0 GLU A 14 4 7.5 4.0 3.0 0.5 0.0 THR A 15 3 13.0 3.0 3.0 7.0 0.0 CYS A 16 0 7.5 3.0 4.5 0.0 0.0 ASP A 17 0 3.5 2.5 1.0 0.0 0.0 ILE A 18 10 18.0 6.0 6.5 5.5 0.0 PRO A 19 0 13.0 7.0 5.5 0.5 0.0 ARG A 20 10 20.5 4.5 5.0 11.0 0.0 GLU A 21 4 11.5 8.0 3.5 0.0 0.0 THR A 22 2 13.5 8.0 5.5 0.0 0.0 ILE A 23 8 26.0 5.5 7.0 13.5 0.0 THR A 24 2 14.5 8.0 3.5 3.0 0.0 PRO A 25 0 17.0 7.0 0.5 9.5 0.0 GLU A 26 6 10.0 4.5 1.5 4.0 0.0 SER A 27 1 11.0 4.0 2.0 5.0 0.0 HIS A 28 1 21.5 3.5 9.5 8.5 0.0 ALA A 29 0 13.5 4.0 4.0 5.5 0.0 ILE A 30 8 14.0 2.5 5.5 6.0 0.0 ASP A 31 0 6.0 1.5 4.5 0.0 0.0 ASP A 32 0 7.5 5.0 1.5 1.0 0.0 LEU A 33 10 21.5 6.5 8.0 7.0 0.0 GLY A 34 0 5.5 3.5 1.5 0.5 0.0 ILE A 35 9 11.0 2.0 4.0 5.0 0.0 ASP A 36 0 8.0 3.5 4.5 0.0 0.0 SER A 37 0 9.0 6.5 2.0 0.5 0.0 LEU A 38 8 11.0 4.0 7.0 0.0 0.0 ASP A 39 0 0.0 0.0 0.0 0.0 0.0 PHE A 40 7 23.5 1.5 10.5 11.5 0.0 LEU A 41 10 9.5 4.0 3.5 2.0 0.0 ASP A 42 0 9.0 5.0 1.5 2.5 0.0 ILE A 43 7 25.5 5.5 11.5 8.5 0.0 ALA A 44 0 17.0 5.0 5.5 6.5 0.0 PHE A 45 4 16.5 5.5 10.5 0.5 0.0 ALA A 46 0 12.5 4.5 6.5 1.5 0.0 ILE A 47 7 32.0 3.0 15.5 13.5 0.0 ASP A 48 1 13.5 4.0 6.5 3.0 0.0 LYS A 49 16 13.0 4.5 8.5 0.0 0.0 ALA A 50 1 15.5 6.5 6.0 3.0 0.0 PHE A 51 6 39.5 6.0 14.5 19.0 0.0 GLY A 52 0 7.5 4.5 2.0 1.0 0.0 ILE A 53 8 39.5 6.5 10.0 23.0 0.0 LYS A 54 10 6.0 5.0 0.0 1.0 0.0 LEU A 55 7 21.0 4.0 3.0 14.0 0.0 PRO A 56 0 7.0 4.0 2.5 0.5 0.0 LEU A 57 7 19.5 4.0 5.0 10.5 0.0 GLU A 58 3 7.0 6.0 1.0 0.0 0.0 LYS A 59 8 11.0 8.5 2.5 0.0 0.0 TRP A 60 2 31.0 8.0 6.0 17.0 0.0 THR A 61 2 11.5 5.5 6.0 0.0 0.0 GLN A 62 11 11.5 5.5 6.0 0.0 0.0 GLU A 63 2 15.0 5.5 3.5 6.0 0.0 VAL A 64 5 20.5 6.5 4.5 9.5 0.0 ASN A 65 6 12.5 4.5 8.0 0.0 0.0 ASP A 66 3 8.0 3.0 5.0 0.0 0.0 GLY A 67 0 7.0 4.5 2.5 0.0 0.0 LYS A 68 20 11.0 5.5 3.0 2.5 0.0 ALA A 69 0 13.0 4.5 3.0 5.5 0.0 THR A 70 2 8.5 3.5 3.5 1.5 0.0 THR A 71 2 8.5 3.0 1.0 4.5 0.0 GLU A 72 3 14.0 4.0 6.0 4.0 0.0 GLN A 73 3 11.0 4.0 5.0 2.0 0.0 TYR A 74 5 14.5 3.5 0.5 10.5 0.0 PHE A 75 2 12.5 4.0 2.0 6.5 0.0 VAL A 76 5 23.5 3.5 14.0 6.0 0.0 LEU A 77 8 25.0 3.5 2.5 19.0 0.0 LYS A 78 9 17.0 4.5 5.0 7.5 0.0 ASN A 79 0 15.5 5.5 7.0 3.0 0.0 LEU A 80 7 25.0 5.0 9.5 10.5 0.0 ALA A 81 1 20.0 4.5 7.0 8.5 0.0 ALA A 82 1 11.0 3.0 7.5 0.5 0.0 ARG A 83 7 21.5 3.5 5.0 13.0 0.0 ILE A 84 8 40.0 5.0 16.5 18.5 0.0 ASP A 85 3 12.5 4.5 7.0 1.0 0.0 GLU A 86 7 11.0 4.5 6.0 0.5 0.0 LEU A 87 10 26.0 6.5 8.0 11.5 0.0 VAL A 88 5 30.5 8.5 14.5 7.5 0.0 ALA A 89 1 11.0 5.0 5.5 0.5 0.0 ALA A 90 1 7.0 2.0 5.0 0.0 0.0 LYS A 91 14 18.5 5.5 9.0 4.0 0.0 GLY A 92 0 7.5 6.5 1.0 0.0 0.0 ALA A 93 1 7.0 4.0 3.0 0.0 0.0 LEU A 94 6 5.0 5.0 0.0 0.0 0.0 GLU A 95 1 5.5 3.5 2.0 0.0 0.0 HIS A 96 0 0.0 0.0 0.0 0.0 0.0 HIS A 97 0 0.0 0.0 0.0 0.0 0.0 HIS A 98 0 0.0 0.0 0.0 0.0 0.0 HIS A 99 0 0.0 0.0 0.0 0.0 0.0 HIS A 100 0 0.0 0.0 0.0 0.0 0.0 HIS A 101 0 0.0 0.0 0.0 0.0 0.0 TOTAL 395 1397.0 431.0 486.0 480.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_