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_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 86 MET GLY HIS HIS HIS HIS HIS HIS SER HIS PRO ASN GLU 1 > ReadCoordsPdb(): Counting models in file `HR3102A_R3Cons_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_R3Cons_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_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 86 > INFO_mol: Radius of Gyration : 13.0046 angstroms > INFO_mol: Center of Masses: x_cm(23.359), y_cm(-32.595), z_cm(-12.209) > 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 `temp.mr' opened for reading 0 SANI-RDC constraints read 97 ACO (dihedral) constraints read 2429 NOE-distance constraints (0 Ambiguous NOE/s) read 2526 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)? :