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 `XCR50_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 09-OCT-04 1XPV > ReadCoordsPdb(): >> TITLE SOLUTION STRUCTURE OF NORTHEAST STRUCTURAL GENOMICS TARGET > ReadCoordsPdb(): >> TITLE 2 PROTEIN XCR50 FROM X. CAMPESTRIS > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN XCC2852; > ReadCoordsPdb(): Counting models in file `XCR50_NMR_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 20 model(s) > ReadCoordsPdb(): what model do you want [(1 to 20) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file XCR50_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 23880 ATOM records read from file > ReadCoordsPdb(): --> 23880 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> > locate_file(): file `XCR50_NMR_em_bcr3.upl' opened for reading > CNSTR_rdr: Converting DYANA UPL input file > CNSTR_rdr: 1540 constraints read PdbStat> > DRAW_cntct: from coordinates or constraints (coor/cons/expected) ?:_ > DRAW_cntct: Making PS file for `XCR50_NMR_em_bcr3.upl.ps' > DRAW_maps: Please enter title for plot (up to 4 lines) > DRAW_maps: To finish just type an asterisk '*' by itself PdbStat> > DRAW_cntct: from coordinates or constraints (coor/cons/expected) ?:_ > MAIN_cntct: What model do you want (1-20) or average ?:_ > do_average_coords(): Making average for backbone atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for backbone onto model 1 > do_average_coords(): Calc. average coordinates backbone > MAIN_cntct: distance cutoff ?:_ > MAIN_cntct: atom type (hydr, heavy, all) ?:_ > CLOSE_cntcts: Contacts for 5.00 angs threshold and HYDR atom type > CLOSE_cntcts: 5474 Close contacts written to file `XCR50_NMR_em_bcr3.upl_Close_cntcts_model21' > MAIN_cntct: Making contact map PS file