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 `STR70_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 ALA ASN ASP THR PRO PHE SER ALA LEU TRP GLN ARG 1 > ReadCoordsPdb(): Counting models in file `STR70_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 STR70_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2249 ATOM records read from file > ReadCoordsPdb(): --> 2249 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2249 (721 C, 1109 H, 210 O, 206 N, 3 S, 0 Q, 0 Metals) > INFO_mol: # residues: 142 (Avg. mol. weight: 113.5) > INFO_mol: # -- M.W. : 16118.9 g/mol. (16.12 kD) Estimated RoG : 14.46 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `STR70_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 142 > INFO_mol: Radius of Gyration : 14.7722 angstroms > INFO_mol: Center of Masses: x_cm(0.044), y_cm(4.329), z_cm(1.242) > INFO_res: MANDTPFSAL WQRLLTRGWQ PVEASTVDDW IKRVGDGVIL LSSDPRRTPE > INFO_res: VSDNPVMIAE LLREFPQFDW QVAVADLEQS EAIGDRFNVR RFPATLVFTD > INFO_res: GKLRGALSGI HPWAELLTLM RSIVDTPAAQ ETVQLEHHHH HH > INFO_res: > INFO_res: MET ALA ASN ASP THR PRO PHE SER ALA LEU TRP GLN > INFO_res: ARG LEU LEU THR ARG GLY TRP GLN PRO VAL GLU ALA > INFO_res: SER THR VAL ASP ASP TRP ILE LYS ARG VAL GLY ASP > INFO_res: GLY VAL ILE LEU LEU SER SER ASP PRO ARG ARG THR > INFO_res: PRO GLU VAL SER ASP ASN PRO VAL MET ILE ALA GLU > INFO_res: LEU LEU ARG GLU PHE PRO GLN PHE ASP TRP GLN VAL > INFO_res: ALA VAL ALA ASP LEU GLU GLN SER GLU ALA ILE GLY > INFO_res: ASP ARG PHE ASN VAL ARG ARG PHE PRO ALA THR LEU > INFO_res: VAL PHE THR ASP GLY LYS LEU ARG GLY ALA LEU SER > INFO_res: GLY ILE HIS PRO TRP ALA GLU LEU LEU THR LEU MET > INFO_res: ARG SER ILE VAL ASP THR PRO ALA ALA GLN GLU THR > INFO_res: VAL GLN LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 12 ALA 11 ARG 3 ASN 11 ASP 7 GLN 9 GLU > INFO_res: 7 GLY 7 HIS 6 ILE 15 LEU 2 LYS 3 MET > INFO_res: 6 PHE 9 PRO 8 SER 9 THR 5 TRP 12 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `temp.mr' opened for reading 69 SANI-RDC constraints read 660 ACO (dihedral) constraints read 1541 NOE-distance constraints (0 Ambiguous NOE/s) read 2270 TOTAL constraints read PdbStat> > WRITER: Output file name ?:_ > WRITER: Coords, constraints, aco or sequence file? :_ > WRITER_constr: Output format (congen | discover | impact | disman | diana | xplor | cns | rosetta)? :