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 `MBR242E_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER DNA BINDING PROTEIN 26-JUN-09 2KKO > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE HOMODIMERIC WINGED HELIX-TURN- > ReadCoordsPdb(): >> TITLE 2 HELIX DNA-BINDING DOMAIN (FRAGMENT 1-100) MB0332 FROM > ReadCoordsPdb(): >> TITLE 3 MYCOBACTERIUM BOVIS, A POSSIBLE ARSR-FAMILY TRANSCRIPTIONAL > ReadCoordsPdb(): >> TITLE 4 REGULATOR. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET 1 > ReadCoordsPdb(): Counting models in file `MBR242E_NMR_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(): Reading *all* models in file MBR242E_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 66560 ATOM records read from file > ReadCoordsPdb(): --> 66560 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> > RMSD_coords : Enter ranges [3-20,25,30-67] ?_ : > RMSD_coords : Reference structure (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 > RMSD_coords : File name for RMSDs (def. `rmsd.pdbstat')?_ : > Kabsch RMSD of backb atoms in res. *[1..226],for model 1 is: 2.289 > Kabsch RMSD of backb atoms in res. *[1..226],for model 2 is: 2.228 > Kabsch RMSD of backb atoms in res. *[1..226],for model 3 is: 2.281 > Kabsch RMSD of backb atoms in res. *[1..226],for model 4 is: 2.235 > Kabsch RMSD of backb atoms in res. *[1..226],for model 5 is: 2.005 > Kabsch RMSD of backb atoms in res. *[1..226],for model 6 is: 1.970 > Kabsch RMSD of backb atoms in res. *[1..226],for model 7 is: 1.660 (*) > Kabsch RMSD of backb atoms in res. *[1..226],for model 8 is: 2.392 > Kabsch RMSD of backb atoms in res. *[1..226],for model 9 is: 1.905 > Kabsch RMSD of backb atoms in res. *[1..226],for model 10 is: 2.144 > Kabsch RMSD of backb atoms in res. *[1..226],for model 11 is: 2.603 > Kabsch RMSD of backb atoms in res. *[1..226],for model 12 is: 2.661 > Kabsch RMSD of backb atoms in res. *[1..226],for model 13 is: 2.437 > Kabsch RMSD of backb atoms in res. *[1..226],for model 14 is: 2.549 > Kabsch RMSD of backb atoms in res. *[1..226],for model 15 is: 2.340 > Kabsch RMSD of backb atoms in res. *[1..226],for model 16 is: 2.575 > Kabsch RMSD of backb atoms in res. *[1..226],for model 17 is: 2.715 > Kabsch RMSD of backb atoms in res. *[1..226],for model 18 is: 2.765 > Kabsch RMSD of backb atoms in res. *[1..226],for model 19 is: 2.733 > Kabsch RMSD of backb atoms in res. *[1..226],for model 20 is: 2.335 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[1..226], is: 2.341 > Range of RMSD values to reference struct. is 1.660 to 2.765 PdbStat> > RMSD_coords : Enter ranges [3-20,25,30-67] ?_ : > RMSD_coords : Reference structure (1-20) or (average) ?_ > do_average_coords(): Making average for heavy atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for heavy onto model 1 > do_average_coords(): Calc. average coordinates heavy > RMSD_coords : File name for RMSDs (def. `rmsd.pdbstat')?_ : > Kabsch RMSD of heavy atoms in res. *[1..226],for model 1 is: 2.842 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 2 is: 2.656 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 3 is: 2.732 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 4 is: 2.928 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 5 is: 2.754 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 6 is: 2.647 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 7 is: 2.314 (*) > Kabsch RMSD of heavy atoms in res. *[1..226],for model 8 is: 2.862 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 9 is: 2.495 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 10 is: 2.748 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 11 is: 3.331 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 12 is: 3.175 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 13 is: 3.103 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 14 is: 3.245 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 15 is: 2.929 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 16 is: 3.006 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 17 is: 3.223 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 18 is: 3.367 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 19 is: 3.308 > Kabsch RMSD of heavy atoms in res. *[1..226],for model 20 is: 2.907 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[1..226], is: 2.929 > Range of RMSD values to reference struct. is 2.314 to 3.367 PdbStat> PdbStat> *END* of program detected, BYE! ...