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 `SGR145_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 31-MAR-10 2KW5 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE SLR1183 PROTEIN FROM > ReadCoordsPdb(): >> TITLE 2 SYNECHOCYSTIS SP. PCC 6803, NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET SGR145 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `SGR145_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 SGR145_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 3141 ATOM records read from file > ReadCoordsPdb(): --> 3141 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 3141 (1007 C, 1560 H, 301 O, 269 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 202 (Avg. mol. weight: 110.8) > INFO_mol: # -- M.W. : 22378.6 g/mol. (22.38 kD) Estimated RoG : 16.54 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SGR145_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 202 > INFO_mol: Radius of Gyration : 19.2422 angstroms > INFO_mol: Center of Masses: x_cm(-0.696), y_cm(-2.013), z_cm(1.253) > INFO_res: MWDERFSQSE YVYGTEPNDF LVSVANQIPQ GKILCLAEGE GRNACFLASL > INFO_res: GYEVTAVDQS SVGLAKAKQL AQEKGVKITT VQSNLADFDI VADAWEGIVS > INFO_res: IFCHLPSSLR QQLYPKVYQG LKPGGVFILE GFAPEQLQYN TGGPKDLDLL > INFO_res: PKLETLQSEL PSLNWLIANN LERNLDEGAY HQGKAALIQL LGQKLEHHHH > INFO_res: HH > INFO_res: > INFO_res: MET TRP ASP GLU ARG PHE SER GLN SER GLU TYR VAL > INFO_res: TYR GLY THR GLU PRO ASN ASP PHE LEU VAL SER VAL > INFO_res: ALA ASN GLN ILE PRO GLN GLY LYS ILE LEU CYS LEU > INFO_res: ALA GLU GLY GLU GLY ARG ASN ALA CYS PHE LEU ALA > INFO_res: SER LEU GLY TYR GLU VAL THR ALA VAL ASP GLN SER > INFO_res: SER VAL GLY LEU ALA LYS ALA LYS GLN LEU ALA GLN > INFO_res: GLU LYS GLY VAL LYS ILE THR THR VAL GLN SER ASN > INFO_res: LEU ALA ASP PHE ASP ILE VAL ALA ASP ALA TRP GLU > INFO_res: GLY ILE VAL SER ILE PHE CYS HIS LEU PRO SER SER > INFO_res: LEU ARG GLN GLN LEU TYR PRO LYS VAL TYR GLN GLY > INFO_res: LEU LYS PRO GLY GLY VAL PHE ILE LEU GLU GLY PHE > INFO_res: ALA PRO GLU GLN LEU GLN TYR ASN THR GLY GLY PRO > INFO_res: LYS ASP LEU ASP LEU LEU PRO LYS LEU GLU THR LEU > INFO_res: GLN SER GLU LEU PRO SER LEU ASN TRP LEU ILE ALA > INFO_res: ASN ASN LEU GLU ARG ASN LEU ASP GLU GLY ALA TYR > INFO_res: HIS GLN GLY LYS ALA ALA LEU ILE GLN LEU LEU GLY > INFO_res: GLN LYS LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 16 ALA 4 ARG 9 ASN 9 ASP 3 CYS 16 GLN > INFO_res: 15 GLU 17 GLY 8 HIS 9 ILE 28 LEU 11 LYS > INFO_res: 1 MET 7 PHE 9 PRO 12 SER 6 THR 7 TYR > INFO_res: 3 TRP 12 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `SGR145_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1011 NOE-distance constraints (0 Ambiguous NOE/s) read 1011 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1011 INTRA-RESIDUE RESTRAINTS (I=J) : 81 SEQUENTIAL RESTRAINTS (I-J)=1 : 220 BACKBONE-BACKBONE : 123 BACKBONE-SIDE CHAIN : 39 SIDE CHAIN-SIDE CHAIN : 58 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 239 BACKBONE-BACKBONE : 103 BACKBONE-SIDE CHAIN : 37 SIDE CHAIN-SIDE CHAIN : 99 LONG RANGE RESTRAINTS (I-J)>=5 : 471 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1011 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 TRP A 2 0 0.0 0.0 0.0 0.0 0.0 ASP A 3 0 0.0 0.0 0.0 0.0 0.0 GLU A 4 0 0.0 0.0 0.0 0.0 0.0 ARG A 5 0 0.0 0.0 0.0 0.0 0.0 PHE A 6 0 0.0 0.0 0.0 0.0 0.0 SER A 7 0 0.0 0.0 0.0 0.0 0.0 GLN A 8 0 0.0 0.0 0.0 0.0 0.0 SER A 9 0 0.0 0.0 0.0 0.0 0.0 GLU A 10 0 0.0 0.0 0.0 0.0 0.0 TYR A 11 0 0.0 0.0 0.0 0.0 0.0 VAL A 12 0 0.0 0.0 0.0 0.0 0.0 TYR A 13 0 0.0 0.0 0.0 0.0 0.0 GLY A 14 0 0.0 0.0 0.0 0.0 0.0 THR A 15 0 0.0 0.0 0.0 0.0 0.0 GLU A 16 0 0.0 0.0 0.0 0.0 0.0 PRO A 17 0 0.0 0.0 0.0 0.0 0.0 ASN A 18 0 0.0 0.0 0.0 0.0 0.0 ASP A 19 0 0.0 0.0 0.0 0.0 0.0 PHE A 20 0 0.0 0.0 0.0 0.0 0.0 LEU A 21 2 11.5 0.0 1.5 10.0 0.0 VAL A 22 2 3.5 1.5 2.0 0.0 0.0 SER A 23 0 4.0 3.0 1.0 0.0 0.0 VAL A 24 2 17.5 3.0 5.5 9.0 0.0 ALA A 25 0 6.5 2.0 2.5 2.0 0.0 ASN A 26 0 5.0 1.0 3.5 0.5 0.0 GLN A 27 0 4.0 1.5 1.0 1.5 0.0 ILE A 28 1 11.0 1.0 3.0 7.0 0.0 PRO A 29 0 0.0 0.0 0.0 0.0 0.0 GLN A 30 0 1.0 0.5 0.5 0.0 0.0 GLY A 31 0 1.5 1.0 0.5 0.0 0.0 LYS A 32 0 2.0 1.0 0.0 1.0 0.0 ILE A 33 1 10.0 1.5 1.0 7.5 0.0 LEU A 34 2 19.0 2.0 2.5 14.5 0.0 CYS A 35 0 5.0 1.5 0.0 3.5 0.0 LEU A 36 1 15.0 1.5 2.0 11.5 0.0 ALA A 37 0 4.5 1.0 0.5 3.0 0.0 GLU A 38 0 0.0 0.0 0.0 0.0 0.0 GLY A 39 0 0.0 0.0 0.0 0.0 0.0 GLU A 40 0 0.0 0.0 0.0 0.0 0.0 GLY A 41 0 0.0 0.0 0.0 0.0 0.0 ARG A 42 0 1.0 0.5 0.5 0.0 0.0 ASN A 43 0 1.5 1.0 0.5 0.0 0.0 ALA A 44 0 2.0 1.0 1.0 0.0 0.0 CYS A 45 0 2.5 1.0 1.0 0.5 0.0 PHE A 46 0 3.0 1.0 1.0 1.0 0.0 LEU A 47 2 19.5 1.5 3.0 15.0 0.0 ALA A 48 0 5.0 1.5 2.0 1.5 0.0 SER A 49 0 4.5 2.0 1.0 1.5 0.0 LEU A 50 2 10.5 2.5 5.5 2.5 0.0 GLY A 51 0 3.0 1.5 0.5 1.0 0.0 TYR A 52 0 2.5 1.0 1.5 0.0 0.0 GLU A 53 0 3.0 1.5 0.0 1.5 0.0 VAL A 54 1 14.5 2.0 2.0 10.5 0.0 THR A 55 0 3.5 1.5 0.0 2.0 0.0 ALA A 56 0 6.0 1.5 0.5 4.0 0.0 VAL A 57 2 19.5 2.5 1.0 16.0 0.0 ASP A 58 0 5.5 1.5 0.5 3.5 0.0 GLN A 59 0 1.5 0.5 0.5 0.5 0.0 SER A 60 0 4.5 0.5 3.5 0.5 0.0 SER A 61 0 2.0 1.5 0.5 0.0 0.0 VAL A 62 2 7.5 3.0 4.5 0.0 0.0 GLY A 63 0 4.5 3.0 1.5 0.0 0.0 LEU A 64 2 14.0 3.0 4.0 7.0 0.0 ALA A 65 0 4.5 2.0 2.5 0.0 0.0 LYS A 66 0 2.5 1.0 1.5 0.0 0.0 ALA A 67 0 2.5 1.0 1.5 0.0 0.0 LYS A 68 0 3.0 1.0 1.5 0.5 0.0 GLN A 69 0 2.0 1.0 1.0 0.0 0.0 LEU A 70 1 4.5 1.0 2.5 1.0 0.0 ALA A 71 0 3.0 1.0 1.0 1.0 0.0 GLN A 72 0 5.0 1.0 3.5 0.5 0.0 GLU A 73 0 3.0 1.0 2.0 0.0 0.0 LYS A 74 0 3.5 1.0 2.5 0.0 0.0 GLY A 75 0 3.0 2.0 1.0 0.0 0.0 VAL A 76 2 11.5 3.0 4.5 4.0 0.0 LYS A 77 0 2.5 2.5 0.0 0.0 0.0 ILE A 78 1 8.0 2.0 1.0 5.0 0.0 THR A 79 0 3.0 1.5 0.0 1.5 0.0 THR A 80 0 3.0 1.5 0.0 1.5 0.0 VAL A 81 2 17.5 2.5 2.0 13.0 0.0 GLN A 82 0 3.5 2.0 0.0 1.5 0.0 SER A 83 0 3.5 1.0 0.5 2.0 0.0 ASN A 84 0 4.0 1.5 1.5 1.0 0.0 LEU A 85 2 15.5 2.0 3.5 10.0 0.0 ALA A 86 0 3.5 1.5 1.0 1.0 0.0 ASP A 87 0 2.5 1.0 1.5 0.0 0.0 PHE A 88 0 4.0 1.0 2.0 1.0 0.0 ASP A 89 0 4.0 1.5 2.0 0.5 0.0 ILE A 90 1 11.5 2.5 0.0 9.0 0.0 VAL A 91 2 10.5 2.5 5.5 2.5 0.0 ALA A 92 0 1.5 1.5 0.0 0.0 0.0 ASP A 93 0 3.0 1.0 2.0 0.0 0.0 ALA A 94 0 3.0 1.5 1.5 0.0 0.0 TRP A 95 0 5.0 1.0 2.0 2.0 0.0 GLU A 96 0 0.0 0.0 0.0 0.0 0.0 GLY A 97 0 1.0 0.0 0.0 1.0 0.0 ILE A 98 0 6.0 0.0 0.0 6.0 0.0 VAL A 99 2 15.0 1.0 2.0 12.0 0.0 SER A 100 0 4.5 2.0 0.0 2.5 0.0 ILE A 101 1 6.5 2.0 2.5 2.0 0.0 PHE A 102 0 3.5 1.5 0.0 2.0 0.0 CYS A 103 0 1.0 0.5 0.5 0.0 0.0 HIS A 104 0 1.0 1.0 0.0 0.0 0.0 LEU A 105 2 9.0 1.0 3.0 5.0 0.0 PRO A 106 0 0.0 0.0 0.0 0.0 0.0 SER A 107 0 2.0 0.5 1.5 0.0 0.0 SER A 108 0 2.5 1.5 1.0 0.0 0.0 LEU A 109 2 11.5 2.5 6.0 3.0 0.0 ARG A 110 0 5.0 2.0 2.0 1.0 0.0 GLN A 111 0 3.5 1.0 2.5 0.0 0.0 GLN A 112 0 3.5 1.0 2.0 0.5 0.0 LEU A 113 2 13.5 2.0 5.0 6.5 0.0 TYR A 114 0 4.5 1.5 2.0 1.0 0.0 PRO A 115 0 0.0 0.0 0.0 0.0 0.0 LYS A 116 0 3.0 1.5 1.0 0.5 0.0 VAL A 117 2 16.0 3.0 6.0 7.0 0.0 TYR A 118 0 3.5 1.5 1.0 1.0 0.0 GLN A 119 0 1.0 0.5 0.5 0.0 0.0 GLY A 120 0 2.5 1.0 1.0 0.5 0.0 LEU A 121 2 12.0 0.5 5.0 6.5 0.0 LYS A 122 0 0.0 0.0 0.0 0.0 0.0 PRO A 123 0 0.0 0.0 0.0 0.0 0.0 GLY A 124 0 3.5 0.5 1.0 2.0 0.0 GLY A 125 0 3.5 1.0 1.0 1.5 0.0 VAL A 126 0 18.0 1.5 2.0 14.5 0.0 PHE A 127 0 6.5 1.0 0.0 5.5 0.0 ILE A 128 1 14.0 1.5 1.5 11.0 0.0 LEU A 129 2 11.5 3.0 0.0 8.5 0.0 GLU A 130 0 3.0 1.5 0.0 1.5 0.0 GLY A 131 0 3.0 0.5 0.0 2.5 0.0 PHE A 132 0 3.0 1.0 0.0 2.0 0.0 ALA A 133 0 4.5 0.5 1.5 2.5 0.0 PRO A 134 0 0.0 0.0 0.0 0.0 0.0 GLU A 135 0 2.5 0.5 1.5 0.5 0.0 GLN A 136 0 4.0 1.5 1.0 1.5 0.0 LEU A 137 2 14.5 2.0 2.5 10.0 0.0 GLN A 138 0 4.5 1.5 1.5 1.5 0.0 TYR A 139 0 2.0 1.0 1.0 0.0 0.0 ASN A 140 0 2.5 1.0 1.5 0.0 0.0 THR A 141 0 1.0 1.0 0.0 0.0 0.0 GLY A 142 0 1.5 1.0 0.5 0.0 0.0 GLY A 143 0 0.5 0.5 0.0 0.0 0.0 PRO A 144 0 0.0 0.0 0.0 0.0 0.0 LYS A 145 0 4.0 0.5 2.5 1.0 0.0 ASP A 146 0 4.5 1.5 2.0 1.0 0.0 LEU A 147 2 12.0 2.0 3.5 6.5 0.0 ASP A 148 0 5.5 2.0 2.5 1.0 0.0 LEU A 149 2 6.5 3.0 3.0 0.5 0.0 LEU A 150 2 12.5 2.0 4.5 6.0 0.0 PRO A 151 0 0.0 0.0 0.0 0.0 0.0 LYS A 152 0 3.0 0.5 2.0 0.5 0.0 LEU A 153 2 12.0 1.5 3.5 7.0 0.0 GLU A 154 0 4.5 1.5 2.0 1.0 0.0 THR A 155 0 3.5 1.0 2.5 0.0 0.0 LEU A 156 2 14.0 2.0 5.0 7.0 0.0 GLN A 157 0 6.5 2.0 2.5 2.0 0.0 SER A 158 0 3.5 1.0 2.0 0.5 0.0 GLU A 159 0 3.5 1.5 1.5 0.5 0.0 LEU A 160 2 14.0 1.0 5.5 7.5 0.0 PRO A 161 0 0.0 0.0 0.0 0.0 0.0 SER A 162 0 3.0 0.5 2.5 0.0 0.0 LEU A 163 2 17.0 1.5 4.5 11.0 0.0 ASN A 164 0 3.5 1.5 0.5 1.5 0.0 TRP A 165 1 8.0 1.5 2.0 4.5 0.0 LEU A 166 2 11.0 4.0 0.5 6.5 0.0 ILE A 167 1 10.0 3.5 0.5 6.0 0.0 ALA A 168 0 2.0 1.0 0.0 1.0 0.0 ASN A 169 0 4.5 1.0 1.5 2.0 0.0 ASN A 170 0 1.5 1.5 0.0 0.0 0.0 LEU A 171 2 7.0 2.0 1.5 3.5 0.0 GLU A 172 0 2.5 1.5 0.0 1.0 0.0 ARG A 173 0 3.0 0.5 0.0 2.5 0.0 ASN A 174 0 1.0 0.5 0.0 0.5 0.0 LEU A 175 2 4.5 0.5 0.0 4.0 0.0 ASP A 176 0 0.0 0.0 0.0 0.0 0.0 GLU A 177 0 0.0 0.0 0.0 0.0 0.0 GLY A 178 0 0.0 0.0 0.0 0.0 0.0 ALA A 179 0 0.0 0.0 0.0 0.0 0.0 TYR A 180 0 0.0 0.0 0.0 0.0 0.0 HIS A 181 0 0.0 0.0 0.0 0.0 0.0 GLN A 182 0 0.0 0.0 0.0 0.0 0.0 GLY A 183 0 0.0 0.0 0.0 0.0 0.0 LYS A 184 0 1.5 0.5 0.0 1.0 0.0 ALA A 185 0 4.5 1.0 1.0 2.5 0.0 ALA A 186 0 3.0 1.5 0.0 1.5 0.0 LEU A 187 2 10.0 3.0 1.0 6.0 0.0 ILE A 188 1 9.5 2.5 1.0 6.0 0.0 GLN A 189 0 4.5 1.5 0.0 3.0 0.0 LEU A 190 2 16.5 2.0 1.5 13.0 0.0 LEU A 191 1 18.0 2.0 0.0 16.0 0.0 GLY A 192 0 6.5 1.5 0.5 4.5 0.0 GLN A 193 0 6.0 1.0 0.5 4.5 0.0 LYS A 194 0 2.5 0.5 0.0 2.0 0.0 LEU A 195 2 5.0 0.5 0.5 4.0 0.0 GLU A 196 0 0.5 0.5 0.0 0.0 0.0 HIS A 197 0 0.0 0.0 0.0 0.0 0.0 HIS A 198 0 0.0 0.0 0.0 0.0 0.0 HIS A 199 0 0.0 0.0 0.0 0.0 0.0 HIS A 200 0 0.0 0.0 0.0 0.0 0.0 HIS A 201 0 0.0 0.0 0.0 0.0 0.0 HIS A 202 0 0.0 0.0 0.0 0.0 0.0 TOTAL 81 930.0 220.0 239.0 471.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_