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 `HR1958_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 143 MET ARG LYS ILE ASP LEU CYS LEU SER SER GLU GLY SER 1 > ReadCoordsPdb(): Counting models in file `HR1958_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 HR1958_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2251 ATOM records read from file > ReadCoordsPdb(): --> 2251 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2251 (725 C, 1110 H, 224 O, 188 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 143 (Avg. mol. weight: 113.1) > INFO_mol: # -- M.W. : 16171.8 g/mol. (16.17 kD) Estimated RoG : 14.50 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `HR1958_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 143 > INFO_mol: Radius of Gyration : 14.6011 angstroms > INFO_mol: Center of Masses: x_cm(-1.841), y_cm(3.495), z_cm(-6.762) > INFO_res: MRKIDLCLSS EGSEVILATS SDEKHPPENI IDGNPETFWT TTGMFPQEFI > INFO_res: ICFHKHVRIE RLVIQSYFVQ TLKIEKSTSK EPVDFEQWIE KDLVHTEGQL > INFO_res: QNEEIVAHGS ATYLRFIIVS AFDHFASVHS VSAEGTVVSN LSS > INFO_res: > INFO_res: MET ARG LYS ILE ASP LEU CYS LEU SER SER GLU GLY > INFO_res: SER GLU VAL ILE LEU ALA THR SER SER ASP GLU LYS > INFO_res: HIS PRO PRO GLU ASN ILE ILE ASP GLY ASN PRO GLU > INFO_res: THR PHE TRP THR THR THR GLY MET PHE PRO GLN GLU > INFO_res: PHE ILE ILE CYS PHE HIS LYS HIS VAL ARG ILE GLU > INFO_res: ARG LEU VAL ILE GLN SER TYR PHE VAL GLN THR LEU > INFO_res: LYS ILE GLU LYS SER THR SER LYS GLU PRO VAL ASP > INFO_res: PHE GLU GLN TRP ILE GLU LYS ASP LEU VAL HIS THR > INFO_res: GLU GLY GLN LEU GLN ASN GLU GLU ILE VAL ALA HIS > INFO_res: GLY SER ALA THR TYR LEU ARG PHE ILE ILE VAL SER > INFO_res: ALA PHE ASP HIS PHE ALA SER VAL HIS SER VAL SER > INFO_res: ALA GLU GLY THR VAL VAL SER ASN LEU SER SER > INFO_res: > INFO_res: 6 ALA 4 ARG 4 ASN 6 ASP 2 CYS 6 GLN > INFO_res: 15 GLU 6 GLY 7 HIS 13 ILE 9 LEU 7 LYS > INFO_res: 2 MET 9 PHE 5 PRO 16 SER 10 THR 2 TYR > INFO_res: 2 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 0 SANI-RDC constraints read 210 ACO (dihedral) constraints read 996 NOE-distance constraints (0 Ambiguous NOE/s) read 1206 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)? :