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 `SR384_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 19 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 18 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 48 MET ILE SER ASN ALA LYS ILE ALA ARG ILE ASN GLU LEU 1 > ReadCoordsPdb(): Counting models in file `SR384_R3Cons_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): I'm reading file SR384_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 787 ATOM records read from file > ReadCoordsPdb(): --> 787 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 787 (237 C, 406 H, 73 O, 69 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 48 (Avg. mol. weight: 113.6) > INFO_mol: # -- M.W. : 5454.3 g/mol. (5.45 kD) Estimated RoG : 9.58 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SR384_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 48 > INFO_mol: Radius of Gyration : 11.7852 angstroms > INFO_mol: Center of Masses: x_cm(4.433), y_cm(-3.154), z_cm(1.070) > INFO_res: MISNAKIARI NELAAKAKAG VITEEEKAEQ QKLRQEYLKG FRSSMKLE > INFO_res: > INFO_res: MET ILE SER ASN ALA LYS ILE ALA ARG ILE ASN GLU > INFO_res: LEU ALA ALA LYS ALA LYS ALA GLY VAL ILE THR GLU > INFO_res: GLU GLU LYS ALA GLU GLN GLN LYS LEU ARG GLN GLU > INFO_res: TYR LEU LYS GLY PHE ARG SER SER MET LYS LEU GLU > INFO_res: > INFO_res: > INFO_res: 7 ALA 3 ARG 2 ASN 3 GLN 7 GLU 2 GLY > INFO_res: 4 ILE 4 LEU 7 LYS 2 MET 1 PHE 3 SER > INFO_res: 1 THR 1 TYR 1 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `SR384_R3Cons_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1023 NOE-distance constraints (0 Ambiguous NOE/s) read 1023 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1023 INTRA-RESIDUE RESTRAINTS (I=J) : 306 SEQUENTIAL RESTRAINTS (I-J)=1 : 207 BACKBONE-BACKBONE : 37 BACKBONE-SIDE CHAIN : 15 SIDE CHAIN-SIDE CHAIN : 155 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 318 BACKBONE-BACKBONE : 70 BACKBONE-SIDE CHAIN : 99 SIDE CHAIN-SIDE CHAIN : 149 LONG RANGE RESTRAINTS (I-J)>=5 : 192 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1023 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 ILE A 2 5 19.5 2.0 6.0 11.5 0.0 SER A 3 0 5.5 2.0 3.5 0.0 0.0 ASN A 4 0 6.0 1.0 5.0 0.0 0.0 ALA A 5 0 4.0 1.5 2.5 0.0 0.0 LYS A 6 15 19.5 3.0 8.5 8.0 0.0 ILE A 7 12 21.0 7.5 11.5 2.0 0.0 ALA A 8 1 13.0 6.0 7.0 0.0 0.0 ARG A 9 16 23.0 4.0 14.0 5.0 0.0 ILE A 10 12 34.0 6.0 9.0 19.0 0.0 ASN A 11 6 17.0 4.5 12.5 0.0 0.0 GLU A 12 6 20.0 7.5 12.5 0.0 0.0 LEU A 13 10 46.0 9.0 17.5 19.5 0.0 ALA A 14 1 14.0 4.0 7.0 3.0 0.0 ALA A 15 1 9.0 2.5 6.5 0.0 0.0 LYS A 16 17 27.0 3.5 12.5 11.0 0.0 ALA A 17 1 15.5 3.0 5.5 7.0 0.0 LYS A 18 14 11.0 4.5 6.5 0.0 0.0 ALA A 19 1 11.5 5.5 6.0 0.0 0.0 GLY A 20 0 10.0 5.0 5.0 0.0 0.0 VAL A 21 2 15.5 5.5 4.0 6.0 0.0 ILE A 22 13 33.5 7.5 6.0 20.0 0.0 THR A 23 2 16.5 8.0 8.5 0.0 0.0 GLU A 24 6 10.0 6.0 4.0 0.0 0.0 GLU A 25 6 9.5 4.0 5.5 0.0 0.0 GLU A 26 7 18.5 2.5 12.5 3.5 0.0 LYS A 27 13 22.5 4.5 9.5 8.5 0.0 ALA A 28 1 12.5 5.0 7.0 0.5 0.0 GLU A 29 8 18.0 6.0 8.5 3.5 0.0 GLN A 30 10 46.0 8.0 17.0 21.0 0.0 GLN A 31 12 15.0 7.0 7.5 0.5 0.0 LYS A 32 17 7.5 4.0 3.5 0.0 0.0 LEU A 33 11 32.0 2.5 14.0 15.5 0.0 ARG A 34 16 29.0 5.5 16.0 7.5 0.0 GLN A 35 10 10.5 6.0 4.5 0.0 0.0 GLU A 36 7 20.0 6.0 7.0 7.0 0.0 TYR A 37 4 27.5 10.5 4.5 12.5 0.0 LEU A 38 11 20.0 9.0 11.0 0.0 0.0 LYS A 39 14 6.0 4.0 2.0 0.0 0.0 GLY A 40 0 1.5 1.5 0.0 0.0 0.0 PHE A 41 3 9.0 2.0 7.0 0.0 0.0 ARG A 42 4 2.0 2.0 0.0 0.0 0.0 SER A 43 0 0.0 0.0 0.0 0.0 0.0 SER A 44 0 0.0 0.0 0.0 0.0 0.0 MET A 45 0 0.0 0.0 0.0 0.0 0.0 LYS A 46 5 1.5 1.5 0.0 0.0 0.0 LEU A 47 4 4.0 4.0 0.0 0.0 0.0 GLU A 48 2 2.5 2.5 0.0 0.0 0.0 TOTAL 306 717.0 207.0 318.0 192.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_