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 `MRR110B_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER DNA BINDING PROTEIN 30-JUN-08 2K5V > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE SECOND OB-FOLD DOMAIN OF > ReadCoordsPdb(): >> TITLE 2 REPLICATION PROTEIN A FROM METHANOCOCCUS MARIPALUDIS. > ReadCoordsPdb(): >> TITLE 3 NORTHEAST STRUCTURAL GENOMICS TARGET MRR110B. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `MRR110B_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 MRR110B_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1527 ATOM records read from file > ReadCoordsPdb(): --> 1527 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1527 (481 C, 769 H, 152 O, 123 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 98 (Avg. mol. weight: 109.9) > INFO_mol: # -- M.W. : 10771.1 g/mol. (10.77 kD) Estimated RoG : 12.56 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `MRR110B_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 98 > INFO_mol: Radius of Gyration : 13.6631 angstroms > INFO_mol: Center of Masses: x_cm(-0.861), y_cm(-0.536), z_cm(0.419) > INFO_res: MNYKISELMP NLSGTINAEV VAAYPKKEFS RKDGTKGQLK SLFLKDDTGS > INFO_res: IRGTLWNELA DFEVKKGDIA EVSGYVKQGY SGLEISVDNI GIIEKSLE > INFO_res: > INFO_res: MET ASN TYR LYS ILE SER GLU LEU MET PRO ASN LEU > INFO_res: SER GLY THR ILE ASN ALA GLU VAL VAL ALA ALA TYR > INFO_res: PRO LYS LYS GLU PHE SER ARG LYS ASP GLY THR LYS > INFO_res: GLY GLN LEU LYS SER LEU PHE LEU LYS ASP ASP THR > INFO_res: GLY SER ILE ARG GLY THR LEU TRP ASN GLU LEU ALA > INFO_res: ASP PHE GLU VAL LYS LYS GLY ASP ILE ALA GLU VAL > INFO_res: SER GLY TYR VAL LYS GLN GLY TYR SER GLY LEU GLU > INFO_res: ILE SER VAL ASP ASN ILE GLY ILE ILE GLU LYS SER > INFO_res: LEU GLU > INFO_res: > INFO_res: 5 ALA 2 ARG 5 ASN 6 ASP 2 GLN 9 GLU > INFO_res: 10 GLY 8 ILE 9 LEU 11 LYS 2 MET 3 PHE > INFO_res: 2 PRO 9 SER 4 THR 4 TYR 1 TRP 6 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `MRR110B_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1700 NOE-distance constraints (0 Ambiguous NOE/s) read 1700 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1700 INTRA-RESIDUE RESTRAINTS (I=J) : 477 SEQUENTIAL RESTRAINTS (I-J)=1 : 441 BACKBONE-BACKBONE : 119 BACKBONE-SIDE CHAIN : 33 SIDE CHAIN-SIDE CHAIN : 289 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 170 BACKBONE-BACKBONE : 30 BACKBONE-SIDE CHAIN : 32 SIDE CHAIN-SIDE CHAIN : 108 LONG RANGE RESTRAINTS (I-J)>=5 : 612 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1700 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 3 2.5 0.0 2.5 0.0 0.0 ASN A 2 0 3.0 2.0 0.0 1.0 0.0 TYR A 3 4 21.0 4.5 3.5 13.0 0.0 LYS A 4 8 13.0 3.0 6.0 4.0 0.0 ILE A 5 12 18.0 3.0 2.0 13.0 0.0 SER A 6 1 9.5 3.0 2.5 4.0 0.0 GLU A 7 3 8.0 3.5 4.5 0.0 0.0 LEU A 8 11 19.0 6.0 5.5 7.5 0.0 MET A 9 6 16.0 7.0 7.0 2.0 0.0 PRO A 10 0 16.0 6.0 0.5 9.5 0.0 ASN A 11 3 8.5 3.5 0.0 5.0 0.0 LEU A 12 13 19.5 5.5 10.5 3.5 0.0 SER A 13 2 8.5 6.5 0.0 2.0 0.0 GLY A 14 0 9.5 4.5 0.5 4.5 0.0 THR A 15 3 17.0 5.0 1.5 10.5 0.0 ILE A 16 10 15.5 5.5 0.5 9.5 0.0 ASN A 17 4 19.5 5.5 1.5 12.5 0.0 ALA A 18 0 12.5 4.0 1.0 7.5 0.0 GLU A 19 2 6.5 2.0 0.0 4.5 0.0 VAL A 20 5 17.5 2.5 1.5 13.5 0.0 VAL A 21 5 20.0 4.5 0.5 15.0 0.0 ALA A 22 0 11.5 4.5 1.5 5.5 0.0 ALA A 23 1 10.0 3.0 1.0 6.0 0.0 TYR A 24 6 13.5 7.0 1.0 5.5 0.0 PRO A 25 0 7.5 7.5 0.0 0.0 0.0 LYS A 26 13 6.0 4.5 0.0 1.5 0.0 LYS A 27 5 12.5 6.5 0.0 6.0 0.0 GLU A 28 6 7.5 6.5 0.0 1.0 0.0 PHE A 29 3 15.5 5.5 2.0 8.0 0.0 SER A 30 3 5.0 5.0 0.0 0.0 0.0 ARG A 31 9 9.5 3.0 5.0 1.5 0.0 LYS A 32 8 4.5 3.5 1.0 0.0 0.0 ASP A 33 3 5.5 4.0 1.5 0.0 0.0 GLY A 34 0 4.0 2.0 2.0 0.0 0.0 THR A 35 2 4.5 3.0 1.5 0.0 0.0 LYS A 36 7 3.5 3.5 0.0 0.0 0.0 GLY A 37 0 5.0 2.0 0.0 3.0 0.0 GLN A 38 7 13.5 3.5 0.0 10.0 0.0 LEU A 39 11 26.0 5.5 1.5 19.0 0.0 LYS A 40 8 16.5 6.5 1.5 8.5 0.0 SER A 41 1 11.5 5.5 1.5 4.5 0.0 LEU A 42 11 13.5 4.0 1.5 8.0 0.0 PHE A 43 6 23.0 5.5 1.0 16.5 0.0 LEU A 44 10 18.0 6.0 0.0 12.0 0.0 LYS A 45 11 22.5 5.5 1.5 15.5 0.0 ASP A 46 0 10.0 4.5 2.0 3.5 0.0 ASP A 47 1 4.5 3.5 1.0 0.0 0.0 THR A 48 2 12.0 3.5 0.5 8.0 0.0 GLY A 49 0 6.5 2.5 2.0 2.0 0.0 SER A 50 0 13.5 3.5 1.0 9.0 0.0 ILE A 51 8 16.5 5.0 0.5 11.0 0.0 ARG A 52 6 11.0 6.5 0.0 4.5 0.0 GLY A 53 0 13.5 5.5 0.5 7.5 0.0 THR A 54 3 13.5 3.0 2.0 8.5 0.0 LEU A 55 10 21.0 4.5 2.5 14.0 0.0 TRP A 56 9 19.5 5.5 4.5 9.5 0.0 ASN A 57 3 10.0 4.5 2.5 3.0 0.0 GLU A 58 3 6.5 4.5 1.0 1.0 0.0 LEU A 59 12 20.0 5.0 10.5 4.5 0.0 ALA A 60 1 19.5 4.0 3.0 12.5 0.0 ASP A 61 3 5.5 4.0 1.5 0.0 0.0 PHE A 62 5 24.5 4.5 8.0 12.0 0.0 GLU A 63 5 6.5 6.5 0.0 0.0 0.0 VAL A 64 4 21.0 7.5 5.5 8.0 0.0 LYS A 65 12 9.5 5.0 2.5 2.0 0.0 LYS A 66 9 13.0 5.0 0.5 7.5 0.0 GLY A 67 0 4.5 3.5 0.0 1.0 0.0 ASP A 68 3 15.0 3.0 5.0 7.0 0.0 ILE A 69 9 17.0 5.5 0.0 11.5 0.0 ALA A 70 0 12.5 4.0 0.5 8.0 0.0 GLU A 71 7 19.5 3.0 0.0 16.5 0.0 VAL A 72 5 17.5 4.0 1.0 12.5 0.0 SER A 73 0 11.5 3.5 0.0 8.0 0.0 GLY A 74 0 9.5 3.0 0.5 6.0 0.0 TYR A 75 4 21.5 6.0 4.5 11.0 0.0 VAL A 76 5 20.5 6.0 0.5 14.0 0.0 LYS A 77 10 15.5 5.5 4.5 5.5 0.0 GLN A 78 7 15.5 8.0 0.5 7.0 0.0 GLY A 79 0 7.0 4.5 2.0 0.5 0.0 TYR A 80 3 3.5 3.0 0.5 0.0 0.0 SER A 81 0 3.5 3.5 0.0 0.0 0.0 GLY A 82 0 3.5 2.5 1.0 0.0 0.0 LEU A 83 11 14.5 3.5 1.5 9.5 0.0 GLU A 84 4 9.0 5.0 0.0 4.0 0.0 ILE A 85 7 22.0 5.5 1.5 15.0 0.0 SER A 86 2 12.0 5.0 0.0 7.0 0.0 VAL A 87 5 16.5 4.5 4.0 8.0 0.0 ASP A 88 0 6.0 3.0 0.0 3.0 0.0 ASN A 89 7 9.0 4.0 1.0 4.0 0.0 ILE A 90 9 24.0 6.0 2.0 16.0 0.0 GLY A 91 0 9.0 5.0 0.0 4.0 0.0 ILE A 92 9 25.0 4.0 6.0 15.0 0.0 ILE A 93 11 18.0 4.5 0.0 13.5 0.0 GLU A 94 2 9.5 5.0 2.0 2.5 0.0 LYS A 95 15 8.5 5.0 3.5 0.0 0.0 SER A 96 0 5.5 5.5 0.0 0.0 0.0 LEU A 97 12 6.0 6.0 0.0 0.0 0.0 GLU A 98 8 3.0 3.0 0.0 0.0 0.0 TOTAL 477 1223.0 441.0 170.0 612.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_