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 `HR3102A_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 86 MET GLY HIS HIS HIS HIS HIS HIS SER HIS PRO ASN GLU 1 > ReadCoordsPdb(): Counting models in file `HR3102A_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 HR3102A_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1364 ATOM records read from file > ReadCoordsPdb(): --> 1364 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1364 (417 C, 682 H, 122 O, 136 N, 7 S, 0 Q, 0 Metals) > INFO_mol: # residues: 86 (Avg. mol. weight: 113.7) > INFO_mol: # -- M.W. : 9777.1 g/mol. (9.78 kD) Estimated RoG : 11.95 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `HR3102A_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 86 > INFO_mol: Radius of Gyration : 13.6848 angstroms > INFO_mol: Center of Masses: x_cm(0.701), y_cm(-2.244), z_cm(1.598) > INFO_res: MGHHHHHHSH PNEEARLDIL KIHSRKMNLT RGINLRKIAE LMPGASGAEV > INFO_res: KGVCTEAGMY ALRERRVHVT QEDFEMAVAK VMQKDS > INFO_res: > INFO_res: MET GLY HIS HIS HIS HIS HIS HIS SER HIS PRO ASN > INFO_res: GLU GLU ALA ARG LEU ASP ILE LEU LYS ILE HIS SER > INFO_res: ARG LYS MET ASN LEU THR ARG GLY ILE ASN LEU ARG > INFO_res: LYS ILE ALA GLU LEU MET PRO GLY ALA SER GLY ALA > INFO_res: GLU VAL LYS GLY VAL CYS THR GLU ALA GLY MET TYR > INFO_res: ALA LEU ARG GLU ARG ARG VAL HIS VAL THR GLN GLU > INFO_res: ASP PHE GLU MET ALA VAL ALA LYS VAL MET GLN LYS > INFO_res: ASP SER > INFO_res: > INFO_res: 8 ALA 7 ARG 3 ASN 3 ASP 1 CYS 2 GLN > INFO_res: 8 GLU 6 GLY 9 HIS 4 ILE 6 LEU 6 LYS > INFO_res: 6 MET 1 PHE 2 PRO 4 SER 3 THR 1 TYR > INFO_res: 6 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `HR3102A_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 2302 NOE-distance constraints (0 Ambiguous NOE/s) read 2302 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 2302 INTRA-RESIDUE RESTRAINTS (I=J) : 462 SEQUENTIAL RESTRAINTS (I-J)=1 : 508 BACKBONE-BACKBONE : 90 BACKBONE-SIDE CHAIN : 61 SIDE CHAIN-SIDE CHAIN : 357 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 707 BACKBONE-BACKBONE : 171 BACKBONE-SIDE CHAIN : 202 SIDE CHAIN-SIDE CHAIN : 334 LONG RANGE RESTRAINTS (I-J)>=5 : 625 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 2302 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 GLY A 2 0 0.0 0.0 0.0 0.0 0.0 HIS A 3 1 0.0 0.0 0.0 0.0 0.0 HIS A 4 0 0.0 0.0 0.0 0.0 0.0 HIS A 5 0 0.0 0.0 0.0 0.0 0.0 HIS A 6 0 0.0 0.0 0.0 0.0 0.0 HIS A 7 0 0.0 0.0 0.0 0.0 0.0 HIS 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 HIS A 10 0 0.0 0.0 0.0 0.0 0.0 PRO A 11 0 9.5 1.0 1.5 7.0 0.0 ASN A 12 0 8.5 4.0 4.5 0.0 0.0 GLU A 13 4 17.0 7.0 5.0 5.0 0.0 GLU A 14 5 14.0 7.0 7.0 0.0 0.0 ALA A 15 1 16.5 5.0 11.5 0.0 0.0 ARG A 16 9 29.5 6.5 11.5 11.5 0.0 LEU A 17 11 51.5 8.5 22.0 21.0 0.0 ASP A 18 3 22.5 7.5 15.0 0.0 0.0 ILE A 19 13 37.0 9.5 18.0 9.5 0.0 LEU A 20 10 52.0 9.0 13.0 30.0 0.0 LYS A 21 21 33.0 7.0 20.5 5.5 0.0 ILE A 22 14 29.5 10.5 19.0 0.0 0.0 HIS A 23 3 19.0 7.0 7.0 5.0 0.0 SER A 24 3 26.5 4.5 13.0 9.0 0.0 ARG A 25 13 21.5 9.5 12.0 0.0 0.0 LYS A 26 13 10.5 9.0 1.5 0.0 0.0 MET A 27 10 29.0 8.0 10.5 10.5 0.0 ASN A 28 6 22.5 9.5 0.0 13.0 0.0 LEU A 29 10 37.0 9.5 14.0 13.5 0.0 THR A 30 3 22.0 7.5 8.0 6.5 0.0 ARG A 31 9 9.5 8.5 1.0 0.0 0.0 GLY A 32 0 7.5 7.5 0.0 0.0 0.0 ILE A 33 11 43.0 6.0 22.5 14.5 0.0 ASN A 34 7 19.0 5.5 8.5 5.0 0.0 LEU A 35 10 43.5 5.0 13.5 25.0 0.0 ARG A 36 14 21.5 7.5 5.0 9.0 0.0 LYS A 37 12 37.0 10.0 20.5 6.5 0.0 ILE A 38 9 52.0 11.5 14.5 26.0 0.0 ALA A 39 1 35.5 8.0 10.0 17.5 0.0 GLU A 40 5 16.0 4.5 8.5 3.0 0.0 LEU A 41 12 30.0 6.5 15.0 8.5 0.0 MET A 42 9 44.0 5.5 14.5 24.0 0.0 PRO A 43 0 7.5 2.5 2.5 2.5 0.0 GLY A 44 0 3.5 2.0 0.0 1.5 0.0 ALA A 45 1 17.0 2.0 9.5 5.5 0.0 SER A 46 0 9.5 4.0 4.0 1.5 0.0 GLY A 47 0 15.0 4.5 5.5 5.0 0.0 ALA A 48 1 11.0 4.0 6.5 0.5 0.0 GLU A 49 6 20.0 6.0 9.5 4.5 0.0 VAL A 50 5 40.5 7.5 11.0 22.0 0.0 LYS A 51 10 24.0 8.0 11.0 5.0 0.0 GLY A 52 0 15.5 6.5 7.0 2.0 0.0 VAL A 53 5 47.0 5.0 14.5 27.5 0.0 CYS A 54 1 21.0 5.5 7.5 8.0 0.0 THR A 55 3 19.5 6.5 11.5 1.5 0.0 GLU A 56 5 32.5 8.0 14.5 10.0 0.0 ALA A 57 1 30.5 6.0 11.0 13.5 0.0 GLY A 58 0 15.5 4.0 7.5 4.0 0.0 MET A 59 10 21.0 6.0 15.0 0.0 0.0 TYR A 60 7 31.5 7.0 15.5 9.0 0.0 ALA A 61 1 34.0 7.5 10.5 16.0 0.0 LEU A 62 9 22.0 9.5 12.0 0.5 0.0 ARG A 63 12 19.0 9.5 9.5 0.0 0.0 GLU A 64 6 20.5 9.0 11.5 0.0 0.0 ARG A 65 8 12.0 7.5 4.5 0.0 0.0 ARG A 66 9 24.5 7.5 10.5 6.5 0.0 VAL A 67 5 15.0 9.5 0.0 5.5 0.0 HIS A 68 3 20.5 9.0 3.5 8.0 0.0 VAL A 69 5 41.0 8.0 5.5 27.5 0.0 THR A 70 2 15.5 5.5 7.5 2.5 0.0 GLN A 71 8 40.0 5.5 7.0 27.5 0.0 GLU A 72 4 13.0 6.5 5.5 1.0 0.0 ASP A 73 1 23.0 5.5 11.0 6.5 0.0 PHE A 74 2 50.0 6.0 8.5 35.5 0.0 GLU A 75 5 23.0 6.0 10.0 7.0 0.0 MET A 76 13 16.5 6.0 7.5 3.0 0.0 ALA A 77 1 30.5 5.5 9.5 15.5 0.0 VAL A 78 5 45.5 7.5 16.0 22.0 0.0 ALA A 79 1 18.0 6.5 9.5 2.0 0.0 LYS A 80 24 19.0 7.5 10.0 1.5 0.0 VAL A 81 5 36.5 11.0 9.5 16.0 0.0 MET A 82 11 26.5 7.0 8.0 11.5 0.0 GLN A 83 4 12.5 4.5 8.0 0.0 0.0 LYS A 84 10 7.5 7.0 0.5 0.0 0.0 ASP A 85 1 5.0 5.0 0.0 0.0 0.0 SER A 86 0 0.5 0.5 0.0 0.0 0.0 TOTAL 462 1840.0 508.0 707.0 625.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_