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 `MBR242E_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 108 MET ALA GLY GLN SER ASP ARG LYS ALA ALA LEU LEU ASP > ReadCoordsPdb(): Counting models in file `MBR242E_R3Cons_em_bcr3.pdb'; Model: > 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 MBR242E_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 3314 ATOM records read from file > ReadCoordsPdb(): --> 3314 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 3314 (1010 C, 1664 H, 306 O, 330 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 216 (Avg. mol. weight: 108.6) > INFO_mol: # -- M.W. : 23453.8 g/mol. (23.45 kD) Estimated RoG : 16.96 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `MBR242E_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 216 > INFO_mol: Radius of Gyration : 19.4058 angstroms > INFO_mol: Center of Masses: x_cm(0.065), y_cm(-0.206), z_cm(0.058) > INFO_res: MAGQSDRKAA LLDQVARVGK ALANGRRLQI LDLLAQGERA VEAIATATGM > INFO_res: NLTTASANLQ ALKSGGLVEA RREGTRQYYR IAGEDVARLF ALVQVVADEH > INFO_res: LEHHHHHHMA GQSDRKAALL DQVARVGKAL ANGRRLQILD LLAQGERAVE > INFO_res: AIATATGMNL TTASANLQAL KSGGLVEARR EGTRQYYRIA GEDVARLFAL > INFO_res: VQVVADEHLE HHHHHH > INFO_res: > INFO_res: MET ALA GLY GLN SER ASP ARG LYS ALA ALA LEU LEU > INFO_res: ASP GLN VAL ALA ARG VAL GLY LYS ALA LEU ALA ASN > INFO_res: GLY ARG ARG LEU GLN ILE LEU ASP LEU LEU ALA GLN > INFO_res: GLY GLU ARG ALA VAL GLU ALA ILE ALA THR ALA THR > INFO_res: GLY MET ASN LEU THR THR ALA SER ALA ASN LEU GLN > INFO_res: ALA LEU LYS SER GLY GLY LEU VAL GLU ALA ARG ARG > INFO_res: GLU GLY THR ARG GLN TYR TYR ARG ILE ALA GLY GLU > INFO_res: ASP VAL ALA ARG LEU PHE ALA LEU VAL GLN VAL VAL > INFO_res: ALA ASP GLU HIS LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: MET ALA GLY GLN SER ASP ARG LYS ALA ALA LEU LEU > INFO_res: ASP GLN VAL ALA ARG VAL GLY LYS ALA LEU ALA ASN > INFO_res: GLY ARG ARG LEU GLN ILE LEU ASP LEU LEU ALA GLN > INFO_res: GLY GLU ARG ALA VAL GLU ALA ILE ALA THR ALA THR > INFO_res: GLY MET ASN LEU THR THR ALA SER ALA ASN LEU GLN > INFO_res: ALA LEU LYS SER GLY GLY LEU VAL GLU ALA ARG ARG > INFO_res: GLU GLY THR ARG GLN TYR TYR ARG ILE ALA GLY GLU > INFO_res: ASP VAL ALA ARG LEU PHE ALA LEU VAL GLN VAL VAL > INFO_res: ALA ASP GLU HIS LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: > INFO_res: 38 ALA 20 ARG 6 ASN 10 ASP 14 GLN 14 GLU > INFO_res: 18 GLY 14 HIS 6 ILE 28 LEU 6 LYS 4 MET > INFO_res: 2 PHE 6 SER 10 THR 4 TYR 16 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `temp.mr' opened for reading 0 SANI-RDC constraints read 336 ACO (dihedral) constraints read 2618 NOE-distance constraints (0 Ambiguous NOE/s) read 206 CHEMICAL SHIFT constraints detected -- not worked out 2954 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)? :