O for Morons

Gerard Kleijwegt gerard at rigel.bmc.uu.se
Fri Feb 11 12:17:40 EST 1994

         "O for Morons - A Beginner's Guide"

"O for Morons" is a tutorial for beginning users of the
macromolecular crystallographic modelling program O.

The tutorial is used in the Uppsala Protein Engineering
course, and will in the future be used for courses in
protein crystallography here.  The tutorial does not
assume previous knowledge of O (or even proteins).  A
basic knowledge of Unix is required ('cp', 'ls' and 'cd'
should be enough, though).  It basically covers the
modelling and analysis facilities in O, including some
very basic "quality control" of protein structures.

Nevertheless, some facilities which are often used in
(protein) crystallography and modelling are explained;
for example:
o  generating a full set of coordinates from only C-alpha
o  rebuilding and "regularising" residues;
o  analysing interactions (hydrogen bonds etc.);
o  mutations, insertions and deletions in existing structures;
o  secondary structure assignment;
o  least-squares superpositioning of different proteins;
o  map handling and surfaces;
o  generating pretty and informative pictures.

(A separate tutorial for crystallographic model
building and rebuilding might get written later.)

There are two ways to obtain the tutorial:

* licensed O users (including commercial users) may
  freely download the complete set of files from the
  O ftp server (the Internet address is listed in the
  O manual); just do:
  ftp> cd pub/moron
  ftp> ascii
  ftp> get README
  ftp> binary
  ftp> get morons.dirtar.Z

* non O users may download the text and figures of the
  tutorial if they want to find out what O can do; in that
  case, ftp to "daisy.bmc.uu.se" (Internet address is, username "ftp", and use your E-mail
  address as the password.  Then:
  ftp> cd pub/moron
  ftp> ascii
  ftp> get README
  ftp> binary
  ftp> get otut.dirtar.Z

The complete tutorial (morons.dirtar.Z) is ~1.6 MB (~4 MB
after uncompressing and un-tar-ing); the text-and-figures-only
version (otut.dirtar.Z) is ~1.2 MB (~3 MB).

In both cases, follow the instructions in the README document.
The figures are provided as PostScript documents; the text
comes in MacWrite II format (my original version), as well as
plain-vanilla ASCII, MicroSoft "Rich-Text-Format" (RTF),
WriteNow (Macintosh), and MS Word (Macintosh) format (some
of these have been "ascii-ised" with BinHex on a Macintosh).

If you are not an O user yet, but would like to become one
(which is very cheap if you work at a University), contact
Prof. Alwyn Jones directly (E-mail "alwyn at xray.bmc.uu.se").

-- Gerard

               Gerard J. Kleywegt              ___  
  Department of Molecular Biology              | |  /\
                Biomedical Centre             /\ -- ||
               Uppsala University             || || ||
                Box 590, S-751 24             || || ||
                  Uppsala, SWEDEN             || \/ --
                                              --  |__|
    E-mail: gerard at xray.bmc.uu.se
           "He's probably pining for the fiords ..."
  The opinions in this mail/post are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
          (Nevertheless, they're mine, mine, MINE !)

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