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 `XCR50_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 78 MET ALA LEU THR LEU TYR GLN ARG ASP ASP CYS HIS LEU > ReadCoordsPdb(): Counting models in file `XCR50_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 XCR50_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1197 ATOM records read from file > ReadCoordsPdb(): --> 1197 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1197 (388 C, 584 H, 113 O, 108 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 78 (Avg. mol. weight: 111.5) > INFO_mol: # -- M.W. : 8697.7 g/mol. (8.70 kD) Estimated RoG : 11.52 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `XCR50_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 78 > INFO_mol: Radius of Gyration : 12.0514 angstroms > INFO_mol: Center of Masses: x_cm(-1.529), y_cm(1.696), z_cm(-0.690) > INFO_res: MALTLYQRDD CHLCDQAVEA LAQARAGAFF SVFIDDDAAL ESAYGLRVPV > INFO_res: LRDPMGRELD WPFDAPRLRA WLDAAPHA > INFO_res: > INFO_res: MET ALA LEU THR LEU TYR GLN ARG ASP ASP CYS HIS > INFO_res: LEU CYS ASP GLN ALA VAL GLU ALA LEU ALA GLN ALA > INFO_res: ARG ALA GLY ALA PHE PHE SER VAL PHE ILE ASP ASP > INFO_res: ASP ALA ALA LEU GLU SER ALA TYR GLY LEU ARG VAL > INFO_res: PRO VAL LEU ARG ASP PRO MET GLY ARG GLU LEU ASP > INFO_res: TRP PRO PHE ASP ALA PRO ARG LEU ARG ALA TRP LEU > INFO_res: ASP ALA ALA PRO HIS ALA > INFO_res: > INFO_res: 15 ALA 7 ARG 10 ASP 2 CYS 3 GLN 3 GLU > INFO_res: 3 GLY 2 HIS 1 ILE 10 LEU 2 MET 4 PHE > INFO_res: 5 PRO 2 SER 1 THR 2 TYR 2 TRP 4 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `XCR50_R3Cons_em_bcr3.upl' opened for reading > CNSTR_rdr: Converting DYANA UPL input file > CNSTR_rdr: 1540 constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1540 INTRA-RESIDUE RESTRAINTS (I=J) : 324 SEQUENTIAL RESTRAINTS (I-J)=1 : 413 BACKBONE-BACKBONE : 96 BACKBONE-SIDE CHAIN : 34 SIDE CHAIN-SIDE CHAIN : 283 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 321 BACKBONE-BACKBONE : 80 BACKBONE-SIDE CHAIN : 82 SIDE CHAIN-SIDE CHAIN : 159 LONG RANGE RESTRAINTS (I-J)>=5 : 482 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1540 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 0 1.0 1.0 0.0 0.0 0.0 ALA A 2 0 5.0 2.0 0.0 3.0 0.0 LEU A 3 7 31.0 5.5 0.5 25.0 0.0 THR A 4 1 18.0 6.5 1.5 10.0 0.0 LEU A 5 6 30.0 5.0 3.5 21.5 0.0 TYR A 6 2 28.0 5.5 1.5 21.0 0.0 GLN A 7 4 13.5 2.5 3.0 8.0 0.0 ARG A 8 0 11.5 2.0 0.0 9.5 0.0 ASP A 9 1 2.0 2.0 0.0 0.0 0.0 ASP A 10 3 2.0 2.0 0.0 0.0 0.0 CYS A 11 0 2.0 2.0 0.0 0.0 0.0 HIS A 12 0 0.0 0.0 0.0 0.0 0.0 LEU A 13 3 9.0 2.0 3.0 4.0 0.0 CYS A 14 0 8.0 4.0 2.0 2.0 0.0 ASP A 15 3 8.0 5.0 3.0 0.0 0.0 GLN A 16 17 18.0 6.5 7.0 4.5 0.0 ALA A 17 1 19.0 5.0 6.0 8.0 0.0 VAL A 18 4 21.0 4.5 10.5 6.0 0.0 GLU A 19 11 16.5 7.0 9.5 0.0 0.0 ALA A 20 0 17.0 6.0 7.0 4.0 0.0 LEU A 21 9 32.5 5.5 9.0 18.0 0.0 ALA A 22 1 12.5 6.0 6.5 0.0 0.0 GLN A 23 11 17.0 5.0 9.0 3.0 0.0 ALA A 24 2 18.5 4.5 3.5 10.5 0.0 ARG A 25 17 8.5 6.0 2.5 0.0 0.0 ALA A 26 1 16.5 6.0 2.5 8.0 0.0 GLY A 27 0 7.0 5.5 0.5 1.0 0.0 ALA A 28 1 5.5 5.5 0.0 0.0 0.0 PHE A 29 3 20.5 4.5 1.0 15.0 0.0 PHE A 30 3 12.5 5.0 1.0 6.5 0.0 SER A 31 3 8.0 6.0 1.5 0.5 0.0 VAL A 32 4 18.0 6.0 2.0 10.0 0.0 PHE A 33 3 10.0 5.5 3.0 1.5 0.0 ILE A 34 9 34.0 7.5 2.5 24.0 0.0 ASP A 35 3 9.0 5.5 3.0 0.5 0.0 ASP A 36 0 3.0 2.5 0.0 0.5 0.0 ASP A 37 4 17.5 5.0 12.5 0.0 0.0 ALA A 38 1 8.5 4.5 4.0 0.0 0.0 ALA A 39 2 8.0 3.5 4.5 0.0 0.0 LEU A 40 8 31.0 6.5 15.5 9.0 0.0 GLU A 41 7 21.0 7.5 7.5 6.0 0.0 SER A 42 5 14.0 7.0 7.0 0.0 0.0 ALA A 43 2 8.0 5.5 2.5 0.0 0.0 TYR A 44 0 28.0 4.0 16.5 7.5 0.0 GLY A 45 3 10.5 2.5 6.0 2.0 0.0 LEU A 46 11 7.0 5.0 1.5 0.5 0.0 ARG A 47 13 14.5 9.0 5.5 0.0 0.0 VAL A 48 4 31.0 7.5 10.0 13.5 0.0 PRO A 49 0 17.5 3.5 0.0 14.0 0.0 VAL A 50 2 24.0 4.0 3.0 17.0 0.0 LEU A 51 8 41.5 7.5 0.0 34.0 0.0 ARG A 52 10 20.5 7.5 0.5 12.5 0.0 ASP A 53 3 20.0 8.0 1.5 10.5 0.0 PRO A 54 0 11.5 8.0 1.0 2.5 0.0 MET A 55 8 10.0 7.0 2.0 1.0 0.0 GLY A 56 0 6.0 4.5 1.5 0.0 0.0 ARG A 57 9 9.5 5.0 2.0 2.5 0.0 GLU A 58 8 18.0 8.0 0.0 10.0 0.0 LEU A 59 5 35.5 8.0 4.5 23.0 0.0 ASP A 60 3 8.0 6.5 0.5 1.0 0.0 TRP A 61 5 20.5 2.5 2.0 16.0 0.0 PRO A 62 0 0.0 0.0 0.0 0.0 0.0 PHE A 63 3 33.5 3.0 16.0 14.5 0.0 ASP A 64 1 17.5 6.5 10.0 1.0 0.0 ALA A 65 1 18.0 9.5 4.0 4.5 0.0 PRO A 66 0 17.0 10.5 6.5 0.0 0.0 ARG A 67 16 31.5 8.0 18.5 5.0 0.0 LEU A 68 7 35.0 7.5 13.0 14.5 0.0 ARG A 69 11 23.5 8.5 8.0 7.0 0.0 ALA A 70 1 12.0 6.5 5.5 0.0 0.0 TRP A 71 7 36.0 7.5 5.0 23.5 0.0 LEU A 72 10 22.5 9.0 10.5 3.0 0.0 ASP A 73 3 9.0 6.0 3.0 0.0 0.0 ALA A 74 1 7.0 4.5 2.5 0.0 0.0 ALA A 75 1 6.0 3.5 1.5 1.0 0.0 PRO A 76 0 5.0 5.0 0.0 0.0 0.0 HIS A 77 7 5.5 5.5 0.0 0.0 0.0 ALA A 78 1 2.0 2.0 0.0 0.0 0.0 TOTAL 324 1216.0 413.0 321.0 482.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_