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 `DHR8C_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 142 MET ASP ASN ARG GLN PHE LEU SER LEU THR GLY VAL SER 1 > ReadCoordsPdb(): Counting models in file `DHR8C_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 DHR8C_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2276 ATOM records read from file > ReadCoordsPdb(): --> 2276 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2276 (720 C, 1148 H, 208 O, 198 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 142 (Avg. mol. weight: 112.5) > INFO_mol: # -- M.W. : 15970.0 g/mol. (15.97 kD) Estimated RoG : 14.46 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `DHR8C_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 142 > INFO_mol: Radius of Gyration : 14.5175 angstroms > INFO_mol: Center of Masses: x_cm(-0.000), y_cm(0.000), z_cm(-0.001) > INFO_res: MDNRQFLSLT GVSKVQSFDP KEILLETIQG VLSIKGEKLG IKHLDLKAGQ > INFO_res: VEVEGLIDAL VYPLEHHHHH HMDNRQFLSL TGVSKVQSFD PKEILLETIQ > INFO_res: GVLSIKGEKL GIKHLDLKAG QVEVEGLIDA LVYPLEHHHH HH > INFO_res: > INFO_res: MET ASP ASN ARG GLN PHE LEU SER LEU THR GLY VAL > INFO_res: SER LYS VAL GLN SER PHE ASP PRO LYS GLU ILE LEU > INFO_res: LEU GLU THR ILE GLN GLY VAL LEU SER ILE LYS GLY > INFO_res: GLU LYS LEU GLY ILE LYS HIS LEU ASP LEU LYS ALA > INFO_res: GLY GLN VAL GLU VAL GLU GLY LEU ILE ASP ALA LEU > INFO_res: VAL TYR PRO LEU GLU HIS HIS HIS HIS HIS HIS MET > INFO_res: ASP ASN ARG GLN PHE LEU SER LEU THR GLY VAL SER > INFO_res: LYS VAL GLN SER PHE ASP PRO LYS GLU ILE LEU LEU > INFO_res: GLU THR ILE GLN GLY VAL LEU SER ILE LYS GLY GLU > INFO_res: LYS LEU GLY ILE LYS HIS LEU ASP LEU LYS ALA GLY > INFO_res: GLN VAL GLU VAL GLU GLY LEU ILE ASP ALA LEU VAL > INFO_res: TYR PRO LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 4 ALA 2 ARG 2 ASN 8 ASP 8 GLN 12 GLU > INFO_res: 12 GLY 14 HIS 10 ILE 22 LEU 12 LYS 2 MET > INFO_res: 4 PHE 4 PRO 8 SER 4 THR 2 TYR 12 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `DHR8C_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1769 NOE-distance constraints (0 Ambiguous NOE/s) read 1769 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1769 INTRA-RESIDUE RESTRAINTS (I=J) : 500 SEQUENTIAL RESTRAINTS (I-J)=1 : 412 BACKBONE-BACKBONE : 148 BACKBONE-SIDE CHAIN : 2 SIDE CHAIN-SIDE CHAIN : 262 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 87 BACKBONE-BACKBONE : 10 BACKBONE-SIDE CHAIN : 19 SIDE CHAIN-SIDE CHAIN : 58 LONG RANGE RESTRAINTS (I-J)>=5 : 770 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1644 INTER-CHAIN RESTRAINTS : 125 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 2 1.5 1.5 0.0 0.0 0.0 ASP A 2 2 3.0 3.0 0.0 0.0 0.0 ASN A 3 3 10.5 3.5 0.0 7.0 3.5 ARG A 4 13 14.0 4.0 0.0 10.0 0.5 GLN A 5 1 20.0 4.0 2.5 13.5 10.5 PHE A 6 2 14.0 3.5 4.5 6.0 4.5 LEU A 7 5 11.5 3.5 1.0 7.0 1.5 SER A 8 3 8.5 4.0 0.0 4.5 2.0 LEU A 9 8 19.5 5.5 6.0 8.0 6.0 THR A 10 1 15.0 4.5 3.5 7.0 6.0 GLY A 11 0 3.0 1.5 0.0 1.5 0.5 VAL A 12 3 10.5 2.5 1.0 7.0 0.0 SER A 13 2 9.0 4.0 0.0 5.0 0.0 LYS A 14 8 8.5 3.0 0.0 5.5 0.0 VAL A 15 3 6.5 2.5 0.0 4.0 0.0 GLN A 16 8 17.0 3.5 0.0 13.5 0.0 SER A 17 0 12.5 4.0 0.0 8.5 0.0 PHE A 18 0 8.0 2.0 0.0 6.0 0.0 ASP A 19 0 0.0 0.0 0.0 0.0 0.0 PRO A 20 0 5.0 1.0 0.0 4.0 0.0 LYS A 21 13 5.0 4.0 0.0 1.0 0.0 GLU A 22 3 11.0 6.0 0.0 5.0 0.0 ILE A 23 8 21.0 5.5 0.0 15.5 0.0 LEU A 24 8 22.0 4.5 0.0 17.5 0.0 LEU A 25 9 17.0 5.0 0.0 12.0 0.0 GLU A 26 4 18.0 5.0 0.0 13.0 0.0 THR A 27 3 18.5 2.5 2.0 14.0 1.5 ILE A 28 9 10.5 2.0 0.0 8.5 8.0 GLN A 29 4 3.0 3.0 0.0 0.0 0.0 GLY A 30 0 3.5 3.0 0.5 0.0 0.0 VAL A 31 5 16.5 4.0 1.5 11.0 0.0 LEU A 32 7 16.5 5.5 0.0 11.0 0.5 SER A 33 0 12.5 4.5 0.0 8.0 0.0 ILE A 34 9 19.0 3.5 0.0 15.5 0.0 LYS A 35 12 16.5 5.0 1.0 10.5 0.0 GLY A 36 0 10.5 4.0 1.5 5.0 0.0 GLU A 37 4 10.0 3.0 0.0 7.0 0.0 LYS A 38 8 9.0 3.0 0.0 6.0 0.0 LEU A 39 8 20.5 3.0 2.5 15.0 0.0 GLY A 40 0 3.0 2.0 0.0 1.0 0.0 ILE A 41 0 0.0 0.0 0.0 0.0 0.0 LYS A 42 0 0.0 0.0 0.0 0.0 0.0 HIS A 43 0 0.0 0.0 0.0 0.0 0.0 LEU A 44 0 0.0 0.0 0.0 0.0 0.0 ASP A 45 0 0.0 0.0 0.0 0.0 0.0 LEU A 46 6 3.5 1.0 0.0 2.5 0.0 LYS A 47 8 3.0 3.0 0.0 0.0 0.0 ALA A 48 1 3.5 3.5 0.0 0.0 0.0 GLY A 49 0 2.0 1.5 0.0 0.5 0.0 GLN A 50 7 7.0 3.0 0.0 4.0 0.0 VAL A 51 5 9.0 4.5 0.0 4.5 0.0 GLU A 52 4 7.0 3.5 0.0 3.5 0.0 VAL A 53 2 5.5 3.5 0.0 2.0 0.0 GLU A 54 1 8.5 3.0 0.0 5.5 0.0 GLY A 55 0 10.0 2.0 0.0 8.0 0.0 LEU A 56 8 25.5 3.0 0.0 22.5 0.0 ILE A 57 8 17.0 4.5 0.0 12.5 1.0 ASP A 58 0 9.5 4.5 0.0 5.0 0.0 ALA A 59 1 11.0 4.0 2.0 5.0 2.0 LEU A 60 7 16.5 3.5 6.5 6.5 7.0 VAL A 61 4 7.0 3.5 0.0 3.5 0.0 TYR A 62 1 14.0 1.5 7.5 5.0 7.5 PRO A 63 0 2.0 2.0 0.0 0.0 0.0 LEU A 64 7 4.5 4.5 0.0 0.0 0.0 GLU A 65 3 4.0 4.0 0.0 0.0 0.0 HIS A 66 0 1.5 1.5 0.0 0.0 0.0 HIS A 67 0 0.0 0.0 0.0 0.0 0.0 HIS A 68 0 0.0 0.0 0.0 0.0 0.0 HIS A 69 0 0.0 0.0 0.0 0.0 0.0 HIS A 70 0 1.0 1.0 0.0 0.0 0.0 HIS A 71 0 1.0 1.0 0.0 0.0 0.0 MET B 1 2 1.5 1.5 0.0 0.0 0.0 ASP B 2 2 3.0 3.0 0.0 0.0 0.0 ASN B 3 3 10.5 3.5 0.0 7.0 3.5 ARG B 4 13 14.0 4.0 0.0 10.0 0.5 GLN B 5 1 20.0 4.0 2.5 13.5 10.5 PHE B 6 2 14.0 3.5 4.5 6.0 4.5 LEU B 7 5 12.0 3.5 1.5 7.0 2.0 SER B 8 1 8.5 4.0 0.0 4.5 2.0 LEU B 9 8 19.0 5.5 5.5 8.0 5.5 THR B 10 1 15.0 4.5 3.5 7.0 6.0 GLY B 11 0 3.0 1.5 0.0 1.5 0.5 VAL B 12 3 10.5 2.5 1.0 7.0 0.0 SER B 13 2 9.0 4.0 0.0 5.0 0.0 LYS B 14 8 8.5 3.0 0.0 5.5 0.0 VAL B 15 3 6.5 2.5 0.0 4.0 0.0 GLN B 16 8 17.0 3.5 0.0 13.5 0.0 SER B 17 0 12.5 4.0 0.0 8.5 0.0 PHE B 18 0 8.0 2.0 0.0 6.0 0.0 ASP B 19 0 0.0 0.0 0.0 0.0 0.0 PRO B 20 0 5.0 1.0 0.0 4.0 0.0 LYS B 21 13 5.0 4.0 0.0 1.0 0.0 GLU B 22 3 11.0 6.0 0.0 5.0 0.0 ILE B 23 8 21.0 5.5 0.0 15.5 0.0 LEU B 24 8 22.0 4.5 0.0 17.5 0.0 LEU B 25 9 17.0 5.0 0.0 12.0 0.0 GLU B 26 4 18.0 5.0 0.0 13.0 0.0 THR B 27 3 18.5 2.5 2.0 14.0 1.5 ILE B 28 9 10.5 2.0 0.0 8.5 8.0 GLN B 29 4 3.0 3.0 0.0 0.0 0.0 GLY B 30 0 3.5 3.0 0.5 0.0 0.0 VAL B 31 5 16.5 4.0 1.5 11.0 0.0 LEU B 32 7 16.5 5.5 0.0 11.0 0.5 SER B 33 0 12.5 4.5 0.0 8.0 0.0 ILE B 34 9 19.0 3.5 0.0 15.5 0.0 LYS B 35 12 16.5 5.0 1.0 10.5 0.0 GLY B 36 0 10.5 4.0 1.5 5.0 0.0 GLU B 37 4 10.0 3.0 0.0 7.0 0.0 LYS B 38 8 9.0 3.0 0.0 6.0 0.0 LEU B 39 8 20.5 3.0 2.5 15.0 0.0 GLY B 40 0 3.0 2.0 0.0 1.0 0.0 ILE B 41 0 0.0 0.0 0.0 0.0 0.0 LYS B 42 0 0.0 0.0 0.0 0.0 0.0 HIS B 43 0 0.0 0.0 0.0 0.0 0.0 LEU B 44 0 0.0 0.0 0.0 0.0 0.0 ASP B 45 0 0.0 0.0 0.0 0.0 0.0 LEU B 46 6 3.5 1.0 0.0 2.5 0.0 LYS B 47 8 3.0 3.0 0.0 0.0 0.0 ALA B 48 1 3.5 3.5 0.0 0.0 0.0 GLY B 49 0 2.0 1.5 0.0 0.5 0.0 GLN B 50 7 7.0 3.0 0.0 4.0 0.0 VAL B 51 5 9.0 4.5 0.0 4.5 0.0 GLU B 52 4 7.0 3.5 0.0 3.5 0.0 VAL B 53 2 5.5 3.5 0.0 2.0 0.0 GLU B 54 1 8.5 3.0 0.0 5.5 0.0 GLY B 55 0 10.0 2.0 0.0 8.0 0.0 LEU B 56 8 25.5 3.0 0.0 22.5 0.0 ILE B 57 8 17.0 4.5 0.0 12.5 1.0 ASP B 58 0 9.5 4.5 0.0 5.0 0.0 ALA B 59 1 11.0 4.0 2.0 5.0 2.0 LEU B 60 7 15.5 3.5 5.5 6.5 6.0 VAL B 61 4 7.0 3.5 0.0 3.5 0.0 TYR B 62 1 15.0 1.5 8.5 5.0 8.5 PRO B 63 0 2.0 2.0 0.0 0.0 0.0 LEU B 64 7 4.5 4.5 0.0 0.0 0.0 GLU B 65 3 4.0 4.0 0.0 0.0 0.0 HIS B 66 0 1.5 1.5 0.0 0.0 0.0 HIS B 67 0 0.0 0.0 0.0 0.0 0.0 HIS B 68 0 0.0 0.0 0.0 0.0 0.0 HIS B 69 0 0.0 0.0 0.0 0.0 0.0 HIS B 70 0 1.0 1.0 0.0 0.0 0.0 HIS B 71 0 1.0 1.0 0.0 0.0 0.0 TOTAL 500 1269.0 412.0 87.0 770.0 125.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_