Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.9 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2013 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.9-exp mar may 14 00:20:00 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 ...) 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 `SPR104_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 82 MET LYS LYS MET ALA GLU PHE THR PHE GLU ILE GLU GLU > ReadCoordsPdb(): Counting models in file `SPR104_R3Cons_em_bcr3.pdb'; Model: > 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 SPR104_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2632 ATOM records read from file > ReadCoordsPdb(): --> 2632 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2632 (852 C, 1282 H, 250 O, 240 N, 8 S, 0 Q, 0 Metals) > INFO_mol: # residues: 164 (Avg. mol. weight: 116.7) > INFO_mol: # -- M.W. : 19143.0 g/mol. (19.14 kD) Estimated RoG : 15.28 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SPR104_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 164 > INFO_mol: Radius of Gyration : 16.3807 angstroms > INFO_mol: Center of Masses: x_cm(-0.065), y_cm(0.362), z_cm(1.869) > INFO_res: MKKMAEFTFE IEEHLLTLSE NEKGWTKEIN RVSFNGAPAK FDIRAWSPDH > INFO_res: TKMGKGITLS NEEFQTMVDA FKGNLEHHHH HHMKKMAEFT FEIEEHLLTL > INFO_res: SENEKGWTKE INRVSFNGAP AKFDIRAWSP DHTKMGKGIT LSNEEFQTMV > INFO_res: DAFKGNLEHH HHHH > INFO_res: > INFO_res: MET LYS LYS MET ALA GLU PHE THR PHE GLU ILE GLU > INFO_res: GLU HIS LEU LEU THR LEU SER GLU ASN GLU LYS GLY > INFO_res: TRP THR LYS GLU ILE ASN ARG VAL SER PHE ASN GLY > INFO_res: ALA PRO ALA LYS PHE ASP ILE ARG ALA TRP SER PRO > INFO_res: ASP HIS THR LYS MET GLY LYS GLY ILE THR LEU SER > INFO_res: ASN GLU GLU PHE GLN THR MET VAL ASP ALA PHE LYS > INFO_res: GLY ASN LEU GLU HIS HIS HIS HIS HIS HIS MET LYS > INFO_res: LYS MET ALA GLU PHE THR PHE GLU ILE GLU GLU HIS > INFO_res: LEU LEU THR LEU SER GLU ASN GLU LYS GLY TRP THR > INFO_res: LYS GLU ILE ASN ARG VAL SER PHE ASN GLY ALA PRO > INFO_res: ALA LYS PHE ASP ILE ARG ALA TRP SER PRO ASP HIS > INFO_res: THR LYS MET GLY LYS GLY ILE THR LEU SER ASN GLU > INFO_res: GLU PHE GLN THR MET VAL ASP ALA PHE LYS GLY ASN > INFO_res: LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 10 ALA 4 ARG 10 ASN 6 ASP 2 GLN 20 GLU > INFO_res: 10 GLY 16 HIS 8 ILE 10 LEU 16 LYS 8 MET > INFO_res: 12 PHE 4 PRO 8 SER 12 THR 4 TRP 4 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `SPR104_R3Cons_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1844 NOE-distance constraints (0 Ambiguous NOE/s) read 1844 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1844 INTRA-RESIDUE RESTRAINTS (I=J) : 468 SEQUENTIAL RESTRAINTS (I-J)=1 : 556 BACKBONE-BACKBONE : 242 BACKBONE-SIDE CHAIN : 10 SIDE CHAIN-SIDE CHAIN : 304 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 140 BACKBONE-BACKBONE : 38 BACKBONE-SIDE CHAIN : 33 SIDE CHAIN-SIDE CHAIN : 69 LONG RANGE RESTRAINTS (I-J)>=5 : 680 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1596 INTER-CHAIN RESTRAINTS : 248 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 0 1.5 1.5 0.0 0.0 0.0 LYS A 2 5 3.0 3.0 0.0 0.0 0.0 LYS A 3 3 3.0 3.0 0.0 0.0 0.0 MET A 4 2 3.0 3.0 0.0 0.0 0.0 ALA A 5 1 2.5 2.5 0.0 0.0 0.0 GLU A 6 2 3.0 3.0 0.0 0.0 0.0 PHE A 7 5 5.0 3.5 0.0 1.5 0.0 THR A 8 3 5.5 3.0 0.0 2.5 0.0 PHE A 9 2 8.5 4.0 0.0 4.5 0.0 GLU A 10 2 8.0 5.0 0.0 3.0 0.0 ILE A 11 11 13.5 4.5 1.0 8.0 0.0 GLU A 12 4 9.5 4.5 0.0 5.0 0.0 GLU A 13 4 11.5 5.0 1.5 5.0 0.0 HIS A 14 2 4.5 3.5 0.0 1.0 0.0 LEU A 15 7 18.5 3.0 0.5 15.0 2.5 LEU A 16 0 19.5 4.0 0.0 15.5 9.5 THR A 17 3 6.0 3.5 0.0 2.5 0.0 LEU A 18 10 21.0 3.0 0.0 18.0 11.5 SER A 19 0 4.0 3.0 0.0 1.0 0.0 GLU A 20 3 8.0 4.0 0.5 3.5 0.0 ASN A 21 0 6.0 4.5 0.5 1.0 0.0 GLU A 22 3 3.5 3.5 0.0 0.0 0.0 LYS A 23 2 2.5 2.5 0.0 0.0 0.0 GLY A 24 0 3.0 1.5 0.5 1.0 0.0 TRP A 25 1 12.0 2.5 0.5 9.0 0.0 THR A 26 2 9.0 3.5 0.0 5.5 0.0 LYS A 27 7 17.0 3.0 0.0 14.0 5.0 GLU A 28 0 6.5 2.5 0.0 4.0 0.0 ILE A 29 5 26.5 2.5 0.0 24.0 4.5 ASN A 30 1 12.0 3.0 0.5 8.5 0.0 ARG A 31 7 16.0 3.5 0.0 12.5 0.0 VAL A 32 5 20.0 4.5 2.5 13.0 0.0 SER A 33 0 9.5 3.5 0.0 6.0 0.0 PHE A 34 2 7.5 2.5 2.0 3.0 0.0 ASN A 35 1 7.5 3.0 0.0 4.5 0.0 GLY A 36 0 2.5 2.5 0.0 0.0 0.0 ALA A 37 1 2.5 2.5 0.0 0.0 0.0 PRO A 38 0 3.5 3.5 0.0 0.0 0.0 ALA A 39 1 12.5 4.0 0.0 8.5 0.0 LYS A 40 5 8.0 4.5 0.0 3.5 0.0 PHE A 41 4 14.5 5.0 0.0 9.5 0.5 ASP A 42 0 10.0 3.0 0.0 7.0 0.0 ILE A 43 8 16.5 1.5 0.0 15.0 0.5 ARG A 44 0 5.0 2.5 0.0 2.5 0.5 ALA A 45 1 10.0 2.5 0.0 7.5 1.0 TRP A 46 1 5.0 2.5 0.0 2.5 0.0 SER A 47 0 2.0 1.5 0.0 0.5 0.0 PRO A 48 0 3.5 0.0 0.0 3.5 0.0 ASP A 49 0 1.5 1.5 0.0 0.0 0.0 HIS A 50 1 2.5 2.5 0.0 0.0 0.0 THR A 51 2 3.0 3.0 0.0 0.0 0.0 LYS A 52 12 8.5 4.5 0.0 4.0 0.0 MET A 53 3 5.5 5.0 0.0 0.5 0.0 GLY A 54 0 4.5 4.0 0.0 0.5 0.0 LYS A 55 9 4.5 3.5 0.5 0.5 0.5 GLY A 56 0 7.5 7.5 0.0 0.0 4.5 ILE A 57 9 19.0 8.5 0.5 10.0 11.0 THR A 58 3 8.5 5.0 0.0 3.5 0.0 LEU A 59 7 11.5 3.5 0.0 8.0 2.0 SER A 60 0 4.0 2.5 0.0 1.5 0.0 ASN A 61 2 6.0 3.0 1.0 2.0 0.5 GLU A 62 5 6.0 4.5 1.5 0.0 0.0 GLU A 63 1 9.0 5.0 2.0 2.0 2.0 PHE A 64 5 19.0 4.5 4.0 10.5 3.0 GLN A 65 10 12.5 4.5 6.0 2.0 2.0 THR A 66 3 12.5 4.5 3.5 4.5 4.5 MET A 67 3 22.5 5.5 6.5 10.5 11.5 VAL A 68 5 25.0 6.0 14.0 5.0 12.5 ASP A 69 1 7.5 4.5 2.5 0.5 0.5 ALA A 70 1 9.5 3.5 2.5 3.5 3.5 PHE A 71 2 23.0 4.0 10.0 9.0 16.5 LYS A 72 12 9.0 5.5 3.5 0.0 4.0 GLY A 73 0 5.5 4.0 1.0 0.5 0.5 ASN A 74 0 3.0 2.5 0.0 0.5 0.5 LEU A 75 6 10.0 2.0 1.0 7.0 7.0 GLU A 76 2 3.5 2.0 0.0 1.5 1.5 HIS A 77 2 3.0 2.5 0.0 0.5 0.5 HIS A 78 1 2.0 2.0 0.0 0.0 0.0 HIS A 79 1 2.0 2.0 0.0 0.0 0.0 HIS A 80 1 1.5 1.5 0.0 0.0 0.0 HIS A 81 1 1.5 1.5 0.0 0.0 0.0 HIS A 82 1 1.0 1.0 0.0 0.0 0.0 MET B 1 0 1.5 1.5 0.0 0.0 0.0 LYS B 2 5 3.0 3.0 0.0 0.0 0.0 LYS B 3 3 3.0 3.0 0.0 0.0 0.0 MET B 4 2 3.0 3.0 0.0 0.0 0.0 ALA B 5 1 2.5 2.5 0.0 0.0 0.0 GLU B 6 2 3.0 3.0 0.0 0.0 0.0 PHE B 7 5 5.0 3.5 0.0 1.5 0.0 THR B 8 3 5.5 3.0 0.0 2.5 0.0 PHE B 9 2 8.5 4.0 0.0 4.5 0.0 GLU B 10 2 8.0 5.0 0.0 3.0 0.0 ILE B 11 11 13.5 4.5 1.0 8.0 0.0 GLU B 12 4 9.5 4.5 0.0 5.0 0.0 GLU B 13 4 11.5 5.0 1.5 5.0 0.0 HIS B 14 2 4.5 3.5 0.0 1.0 0.0 LEU B 15 7 18.5 3.0 0.5 15.0 2.5 LEU B 16 0 19.5 4.0 0.0 15.5 9.5 THR B 17 3 6.0 3.5 0.0 2.5 0.0 LEU B 18 10 21.0 3.0 0.0 18.0 11.5 SER B 19 0 4.0 3.0 0.0 1.0 0.0 GLU B 20 3 8.0 4.0 0.5 3.5 0.0 ASN B 21 0 6.0 4.5 0.5 1.0 0.0 GLU B 22 3 3.5 3.5 0.0 0.0 0.0 LYS B 23 2 2.5 2.5 0.0 0.0 0.0 GLY B 24 0 3.0 1.5 0.5 1.0 0.0 TRP B 25 1 12.0 2.5 0.5 9.0 0.0 THR B 26 2 9.0 3.5 0.0 5.5 0.0 LYS B 27 7 17.0 3.0 0.0 14.0 5.0 GLU B 28 0 6.5 2.5 0.0 4.0 0.0 ILE B 29 5 26.5 2.5 0.0 24.0 4.5 ASN B 30 1 12.0 3.0 0.5 8.5 0.0 ARG B 31 7 16.0 3.5 0.0 12.5 0.0 VAL B 32 5 20.0 4.5 2.5 13.0 0.0 SER B 33 0 9.5 3.5 0.0 6.0 0.0 PHE B 34 2 7.5 2.5 2.0 3.0 0.0 ASN B 35 1 7.5 3.0 0.0 4.5 0.0 GLY B 36 0 2.5 2.5 0.0 0.0 0.0 ALA B 37 1 2.5 2.5 0.0 0.0 0.0 PRO B 38 0 3.5 3.5 0.0 0.0 0.0 ALA B 39 1 12.5 4.0 0.0 8.5 0.0 LYS B 40 5 8.0 4.5 0.0 3.5 0.0 PHE B 41 4 14.5 5.0 0.0 9.5 0.5 ASP B 42 0 10.0 3.0 0.0 7.0 0.0 ILE B 43 8 16.5 1.5 0.0 15.0 0.5 ARG B 44 0 5.0 2.5 0.0 2.5 0.5 ALA B 45 1 10.0 2.5 0.0 7.5 1.0 TRP B 46 1 5.0 2.5 0.0 2.5 0.0 SER B 47 0 2.0 1.5 0.0 0.5 0.0 PRO B 48 0 3.5 0.0 0.0 3.5 0.0 ASP B 49 0 1.5 1.5 0.0 0.0 0.0 HIS B 50 1 2.5 2.5 0.0 0.0 0.0 THR B 51 2 3.0 3.0 0.0 0.0 0.0 LYS B 52 12 8.5 4.5 0.0 4.0 0.0 MET B 53 3 5.5 5.0 0.0 0.5 0.0 GLY B 54 0 4.5 4.0 0.0 0.5 0.0 LYS B 55 9 4.5 3.5 0.5 0.5 0.5 GLY B 56 0 7.5 7.5 0.0 0.0 4.5 ILE B 57 7 19.0 8.5 0.5 10.0 11.0 THR B 58 3 8.5 5.0 0.0 3.5 0.0 LEU B 59 7 11.5 3.5 0.0 8.0 2.0 SER B 60 0 4.0 2.5 0.0 1.5 0.0 ASN B 61 2 6.0 3.0 1.0 2.0 0.5 GLU B 62 5 6.0 4.5 1.5 0.0 0.0 GLU B 63 1 9.0 5.0 2.0 2.0 2.0 PHE B 64 5 19.0 4.5 4.0 10.5 3.0 GLN B 65 10 12.5 4.5 6.0 2.0 2.0 THR B 66 3 12.5 4.5 3.5 4.5 4.5 MET B 67 3 22.5 5.5 6.5 10.5 11.5 VAL B 68 5 25.0 6.0 14.0 5.0 12.5 ASP B 69 1 7.5 4.5 2.5 0.5 0.5 ALA B 70 1 9.5 3.5 2.5 3.5 3.5 PHE B 71 2 23.0 4.0 10.0 9.0 16.5 LYS B 72 8 9.0 5.5 3.5 0.0 4.0 GLY B 73 0 5.5 4.0 1.0 0.5 0.5 ASN B 74 0 3.0 2.5 0.0 0.5 0.5 LEU B 75 6 10.0 2.0 1.0 7.0 7.0 GLU B 76 2 3.5 2.0 0.0 1.5 1.5 HIS B 77 2 3.0 2.5 0.0 0.5 0.5 HIS B 78 1 2.0 2.0 0.0 0.0 0.0 HIS B 79 1 2.0 2.0 0.0 0.0 0.0 HIS B 80 1 1.5 1.5 0.0 0.0 0.0 HIS B 81 1 1.5 1.5 0.0 0.0 0.0 HIS B 82 1 1.0 1.0 0.0 0.0 0.0 TOTAL 468 1376.0 556.0 140.0 680.0 248.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_