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 `SGR209C_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER PROTEIN BINDING 30-JUN-10 2L06 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE PBS LINKER POLYPEPTIDE DOMAIN (FRAGMENT > ReadCoordsPdb(): >> TITLE 2 254-400) OF PHYCOBILISOME LINKER PROTEIN APCE FROM SYNECHOCYSTIS SP. > ReadCoordsPdb(): >> TITLE 3 PCC 6803. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SGR209C > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `SGR209C_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 SGR209C_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2517 ATOM records read from file > ReadCoordsPdb(): --> 2517 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2517 (806 C, 1253 H, 229 O, 227 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 155 (Avg. mol. weight: 115.2) > INFO_mol: # -- M.W. : 17850.9 g/mol. (17.85 kD) Estimated RoG : 14.95 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SGR209C_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 155 > INFO_mol: Radius of Gyration : 16.6757 angstroms > INFO_mol: Center of Masses: x_cm(-1.142), y_cm(-2.549), z_cm(-0.737) > INFO_res: PQSYFNAAAK RQKYAMKPGL SALEKNAVIK AAYRQIFERD ITKAYSQSIS > INFO_res: YLESQVRNGD ISMKEFVRRL AKSPLYRKQF FEPFINSRAL ELAFRHILGR > INFO_res: GPSSREEVQK YFSIVSSGGL PALVDALVDS QEYADYFGEE TVPYLRGLEH > INFO_res: HHHHH > INFO_res: > INFO_res: PRO GLN SER TYR PHE ASN ALA ALA ALA LYS ARG GLN > INFO_res: LYS TYR ALA MET LYS PRO GLY LEU SER ALA LEU GLU > INFO_res: LYS ASN ALA VAL ILE LYS ALA ALA TYR ARG GLN ILE > INFO_res: PHE GLU ARG ASP ILE THR LYS ALA TYR SER GLN SER > INFO_res: ILE SER TYR LEU GLU SER GLN VAL ARG ASN GLY ASP > INFO_res: ILE SER MET LYS GLU PHE VAL ARG ARG LEU ALA LYS > INFO_res: SER PRO LEU TYR ARG LYS GLN PHE PHE GLU PRO PHE > INFO_res: ILE ASN SER ARG ALA LEU GLU LEU ALA PHE ARG HIS > INFO_res: ILE LEU GLY ARG GLY PRO SER SER ARG GLU GLU VAL > INFO_res: GLN LYS TYR PHE SER ILE VAL SER SER GLY GLY LEU > INFO_res: PRO ALA LEU VAL ASP ALA LEU VAL ASP SER GLN GLU > INFO_res: TYR ALA ASP TYR PHE GLY GLU GLU THR VAL PRO TYR > INFO_res: LEU ARG GLY LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 15 ALA 12 ARG 4 ASN 5 ASP 8 GLN 12 GLU > INFO_res: 8 GLY 7 HIS 8 ILE 13 LEU 10 LYS 2 MET > INFO_res: 9 PHE 7 PRO 15 SER 2 THR 10 TYR 8 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `SGR209C_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1790 NOE-distance constraints (0 Ambiguous NOE/s) read 1790 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1790 INTRA-RESIDUE RESTRAINTS (I=J) : 497 SEQUENTIAL RESTRAINTS (I-J)=1 : 465 BACKBONE-BACKBONE : 122 BACKBONE-SIDE CHAIN : 18 SIDE CHAIN-SIDE CHAIN : 325 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 399 BACKBONE-BACKBONE : 106 BACKBONE-SIDE CHAIN : 117 SIDE CHAIN-SIDE CHAIN : 176 LONG RANGE RESTRAINTS (I-J)>=5 : 429 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1790 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain PRO A 1 0 0.0 0.0 0.0 0.0 0.0 GLN A 2 0 0.0 0.0 0.0 0.0 0.0 SER A 3 0 0.0 0.0 0.0 0.0 0.0 TYR A 4 0 0.0 0.0 0.0 0.0 0.0 PHE A 5 0 0.0 0.0 0.0 0.0 0.0 ASN A 6 0 0.0 0.0 0.0 0.0 0.0 ALA A 7 0 0.0 0.0 0.0 0.0 0.0 ALA A 8 0 0.0 0.0 0.0 0.0 0.0 ALA A 9 0 0.0 0.0 0.0 0.0 0.0 LYS A 10 1 1.0 1.0 0.0 0.0 0.0 ARG A 11 6 2.5 2.5 0.0 0.0 0.0 GLN A 12 6 3.5 3.5 0.0 0.0 0.0 LYS A 13 7 6.0 4.5 0.0 1.5 0.0 TYR A 14 2 18.0 5.0 0.0 13.0 0.0 ALA A 15 1 12.5 4.5 0.5 7.5 0.0 MET A 16 9 19.5 4.0 1.5 14.0 0.0 LYS A 17 5 7.5 3.5 4.0 0.0 0.0 PRO A 18 0 3.5 3.5 0.0 0.0 0.0 GLY A 19 0 2.5 2.5 0.0 0.0 0.0 LEU A 20 9 16.0 3.0 9.0 4.0 0.0 SER A 21 1 8.5 5.0 3.5 0.0 0.0 ALA A 22 1 7.5 4.0 3.5 0.0 0.0 LEU A 23 11 9.0 4.0 5.0 0.0 0.0 GLU A 24 4 12.5 4.5 8.0 0.0 0.0 LYS A 25 10 14.0 3.5 5.5 5.0 0.0 ASN A 26 2 11.0 4.0 7.0 0.0 0.0 ALA A 27 1 8.5 4.5 3.0 1.0 0.0 VAL A 28 5 21.5 3.5 4.0 14.0 0.0 ILE A 29 8 18.0 3.0 6.0 9.0 0.0 LYS A 30 4 6.5 3.0 3.5 0.0 0.0 ALA A 31 1 11.0 3.5 3.0 4.5 0.0 ALA A 32 1 11.0 2.5 2.5 6.0 0.0 TYR A 33 3 9.5 2.0 3.5 4.0 0.0 ARG A 34 5 7.0 4.0 2.0 1.0 0.0 GLN A 35 1 4.0 3.0 0.5 0.5 0.0 ILE A 36 8 13.0 2.5 1.5 9.0 0.0 PHE A 37 1 8.0 3.5 3.5 1.0 0.0 GLU A 38 2 5.5 3.0 2.5 0.0 0.0 ARG A 39 4 6.5 3.5 2.0 1.0 0.0 ASP A 40 2 2.5 2.5 0.0 0.0 0.0 ILE A 41 8 15.5 3.0 8.5 4.0 0.0 THR A 42 2 6.5 5.5 1.0 0.0 0.0 LYS A 43 5 4.5 4.5 0.0 0.0 0.0 ALA A 44 1 4.5 4.5 0.0 0.0 0.0 TYR A 45 3 12.0 4.0 6.5 1.5 0.0 SER A 46 1 5.0 1.0 4.0 0.0 0.0 GLN A 47 2 1.5 1.5 0.0 0.0 0.0 SER A 48 0 5.0 4.0 1.0 0.0 0.0 ILE A 49 10 18.0 5.0 7.5 5.5 0.0 SER A 50 1 4.5 3.5 1.0 0.0 0.0 TYR A 51 4 6.0 3.5 2.5 0.0 0.0 LEU A 52 10 20.0 5.0 5.0 10.0 0.0 GLU A 53 0 8.5 3.5 2.5 2.5 0.0 SER A 54 1 4.0 2.5 1.5 0.0 0.0 GLN A 55 5 13.5 4.5 4.5 4.5 0.0 VAL A 56 5 22.5 5.5 3.5 13.5 0.0 ARG A 57 6 8.5 4.5 1.0 3.0 0.0 ASN A 58 4 7.0 3.5 3.5 0.0 0.0 GLY A 59 0 5.5 2.0 2.5 1.0 0.0 ASP A 60 1 5.5 2.0 2.0 1.5 0.0 ILE A 61 4 17.0 4.0 1.5 11.5 0.0 SER A 62 0 5.5 2.5 2.0 1.0 0.0 MET A 63 4 14.5 1.0 3.5 10.0 0.0 LYS A 64 4 10.0 2.5 4.0 3.5 0.0 GLU A 65 1 3.5 2.0 1.5 0.0 0.0 PHE A 66 4 21.5 3.0 5.5 13.0 0.0 VAL A 67 5 22.5 6.0 7.0 9.5 0.0 ARG A 68 2 10.0 4.0 1.5 4.5 0.0 ARG A 69 4 5.5 1.5 0.5 3.5 0.0 LEU A 70 7 19.5 2.5 8.0 9.0 0.0 ALA A 71 1 9.5 2.5 2.0 5.0 0.0 LYS A 72 5 5.0 2.5 0.5 2.0 0.0 SER A 73 2 6.5 3.5 3.0 0.0 0.0 PRO A 74 0 5.5 4.0 1.5 0.0 0.0 LEU A 75 8 11.0 3.0 5.5 2.5 0.0 TYR A 76 0 2.0 1.5 0.5 0.0 0.0 ARG A 77 8 6.0 2.0 2.0 2.0 0.0 LYS A 78 7 6.0 3.0 3.0 0.0 0.0 GLN A 79 5 7.5 3.5 4.0 0.0 0.0 PHE A 80 3 5.0 2.5 0.0 2.5 0.0 PHE A 81 1 8.5 2.0 2.0 4.5 0.0 GLU A 82 2 4.5 3.0 1.5 0.0 0.0 PRO A 83 0 5.0 4.5 0.5 0.0 0.0 PHE A 84 1 11.0 6.0 3.0 2.0 0.0 ILE A 85 7 6.5 4.0 2.5 0.0 0.0 ASN A 86 2 5.5 2.0 1.0 2.5 0.0 SER A 87 0 5.0 1.5 3.0 0.5 0.0 ARG A 88 5 6.0 2.5 3.5 0.0 0.0 ALA A 89 1 9.5 3.5 2.0 4.0 0.0 LEU A 90 9 25.0 4.0 5.5 15.5 0.0 GLU A 91 4 8.5 4.0 2.5 2.0 0.0 LEU A 92 8 8.5 3.5 2.5 2.5 0.0 ALA A 93 1 10.0 4.0 3.0 3.0 0.0 PHE A 94 3 19.5 3.5 9.5 6.5 0.0 ARG A 95 5 8.0 4.0 1.5 2.5 0.0 HIS A 96 1 6.0 4.0 1.5 0.5 0.0 ILE A 97 11 18.5 3.0 3.0 12.5 0.0 LEU A 98 9 14.5 4.0 4.5 6.0 0.0 GLY A 99 0 5.0 3.0 1.0 1.0 0.0 ARG A 100 1 6.0 3.0 1.5 1.5 0.0 GLY A 101 0 4.0 3.5 0.0 0.5 0.0 PRO A 102 0 6.5 1.5 0.5 4.5 0.0 SER A 103 0 1.5 1.5 0.0 0.0 0.0 SER A 104 0 5.0 1.0 4.0 0.0 0.0 ARG A 105 8 4.0 2.0 2.0 0.0 0.0 GLU A 106 4 5.0 3.5 1.5 0.0 0.0 GLU A 107 3 9.5 3.0 5.5 1.0 0.0 VAL A 108 5 15.5 5.0 7.0 3.5 0.0 GLN A 109 7 8.5 5.5 3.0 0.0 0.0 LYS A 110 8 10.0 6.0 4.0 0.0 0.0 TYR A 111 5 25.5 5.0 9.0 11.5 0.0 PHE A 112 4 18.0 2.5 10.0 5.5 0.0 SER A 113 1 3.5 2.5 1.0 0.0 0.0 ILE A 114 12 20.5 4.0 9.5 7.0 0.0 VAL A 115 5 20.0 4.5 6.0 9.5 0.0 SER A 116 2 3.5 2.5 1.0 0.0 0.0 SER A 117 1 4.5 2.0 2.0 0.5 0.0 GLY A 118 0 3.5 1.5 2.0 0.0 0.0 GLY A 119 0 3.5 0.5 3.0 0.0 0.0 LEU A 120 6 10.5 2.5 1.5 6.5 0.0 PRO A 121 0 9.5 4.5 3.5 1.5 0.0 ALA A 122 1 10.0 3.0 4.0 3.0 0.0 LEU A 123 6 23.0 4.0 5.0 14.0 0.0 VAL A 124 5 16.5 5.5 6.5 4.5 0.0 ASP A 125 2 9.5 4.0 5.0 0.5 0.0 ALA A 126 1 8.0 2.5 3.0 2.5 0.0 LEU A 127 9 28.0 3.5 8.0 16.5 0.0 VAL A 128 5 19.5 4.5 4.5 10.5 0.0 ASP A 129 1 6.0 3.5 2.0 0.5 0.0 SER A 130 3 9.0 3.5 5.5 0.0 0.0 GLN A 131 6 6.0 3.0 3.0 0.0 0.0 GLU A 132 3 5.0 2.0 3.0 0.0 0.0 TYR A 133 4 11.5 3.5 3.0 5.0 0.0 ALA A 134 1 8.5 3.5 5.0 0.0 0.0 ASP A 135 1 4.5 3.0 1.5 0.0 0.0 TYR A 136 4 5.0 3.5 1.5 0.0 0.0 PHE A 137 0 4.0 2.5 1.5 0.0 0.0 GLY A 138 0 3.5 2.0 1.5 0.0 0.0 GLU A 139 2 4.5 2.5 0.0 2.0 0.0 GLU A 140 4 8.0 2.5 0.5 5.0 0.0 THR A 141 3 7.0 2.5 1.5 3.0 0.0 VAL A 142 4 16.5 3.0 0.0 13.5 0.0 PRO A 143 0 6.0 3.0 0.0 3.0 0.0 TYR A 144 1 8.0 4.5 2.0 1.5 0.0 LEU A 145 9 9.0 6.0 0.0 3.0 0.0 ARG A 146 4 4.5 4.0 0.5 0.0 0.0 GLY A 147 0 2.0 2.0 0.0 0.0 0.0 LEU A 148 7 3.5 3.5 0.0 0.0 0.0 GLU A 149 5 3.5 3.5 0.0 0.0 0.0 HIS A 150 0 1.0 1.0 0.0 0.0 0.0 HIS A 151 0 0.0 0.0 0.0 0.0 0.0 HIS A 152 0 0.0 0.0 0.0 0.0 0.0 HIS A 153 0 0.0 0.0 0.0 0.0 0.0 HIS A 154 0 0.0 0.0 0.0 0.0 0.0 HIS A 155 0 0.0 0.0 0.0 0.0 0.0 TOTAL 497 1293.0 465.0 399.0 429.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_