Protein model rebuilding tutorial (using O) available

Gerard 'CD' Kleywegt GERARD at XRAY.BMC.UU.SE
Fri Jan 19 12:27:52 EST 1996


A tutorial for protein model rebuilding with O (and some refinement with X-PLOR)
is now available via anonymous ftp from (; note
that this is *not* the regular O ftp server [lack of diskspace]), in directory
pub/tutorial as file rebtut.dirtar.Z.  When uncompressed and tar-ed, this
will create a directory rebtut which contains a README file, the text of the
tutorial (in plain ASCII, HTML and PostScript format) and a directory tree
called gmrp which the students have to copy (cp -r) to their own work area.

The tutorial contains 10 chapters:

 ** OOPS

The title of the tutorial was decided by popular vote and is:

                     O for the Structurally Challenged
a name which was suggested by Kurt Watkins in Dallas (the prize is in the mail).

--Gerard Kleywegt

The text below is taken from the introduction:


 This is a tutorial to introduce protein-model rebuilding and quality
   control using O, and refinement using X-PLOR.  It requires the following:
 - basic familiarity with O (e.g., through the "O for Morons" tutorial)
 - O version 5.10.x and an O manual
 - a few files provided with this tutorial
 - access to the O public domain directory (generically called OMAC; check
   the correct name on your local system; if not present, get it from the
   O ftp server, file "pub/gerard/omac.dirtar.Z")
 - the list of Frequently-Asked Questions (file "OMAC/software.faq"; also
   available through the WorldWide Web)
 - some Uppsala utility programs (also available from the O ftp server;
   you will also need the manuals for these programs)
 - X-PLOR (version 3.1 or 4) and the X-PLOR manual
 - CCP4 programs (not necessary; they are used for map calculations,
   but these can also be carried out with X-PLOR)

 The tutorial can be used in different ways:
 - as a quick introduction to quality control and rebuilding:
   chapters 2, 3, 4 and 5 (optionally, 8 and 9);
 - as a quick introduction to refinement (only for absolute X-PLOR
   beginners): chapters 6 and 7;
 - as a complete course in rebuilding and refinement from first
   to final model: all chapters (including several iterations
   of chapter 9).

 Chapters 5, 7 and 9 will generally be the most time-consuming (depending
   on the level of experience the student has with O and rebuilding and
   refinement in general).  Chapters 2 to 8 contain a few questions in
   sections called "The Swedish Inquisition".  Generally, these will
   aid or extend the understanding of the subject matter covered in that

 In addition, ask your system manager to install the "run", "ono" and
   "oplot" scripts (from the server, directory pub/gerard/scripts); these
   will make your O-life a tad simpler.

 The tutorial does not include ab initio model-building in an MIR map.
   For this purpose, there are some macros on the O ftp server (directory

 Also, the structure used as an example has no NCS, so averaging is not
   covered either.  There is, however, a separate RAVE tutorial available
   from the O ftp server (file "pub/gerard/rave/exam.dirtar.Z").

 The structure you will be working with is that of cellular retinoic-acid
   binding protein type II (CRABP II) in complex with all-trans-retinoic
   acid.  This structure was solved at 1.8 \A, but we will only use data
   to 2.8 \A initially to show the effects that limited resolution may have.
   Our starting model is derived from a related protein, CRABPI, which was
   solved at 2.9 \A resolution.  This structure was changed as follows:
 - the N and C terminal residues were removed
 - the region near the insertion in CRABPII was removed (114-117)
 - a loop with poor density and high temperature factors was
   removed  (100-106)
 - residues which differ between CRABPI and II were cut back to alanines
   (unless they are glycines in CRABPI)

 The temperature factors of this model were reset, and it was subjected
   to mild Simulated Annealing refinement etc.  I then "rebuilt" it to
   introduce some deliberate errors and did some more energy minimisation
   and individual temperature-factor refinement.  After this, a 2Fo-Fc
   and an Fo-Fc map were calculated.

 This structure has the advantage that it is fairly small and yet has
   most of the common errors and problems (main chain, side chain,
   poor loop, insertion site, low resolution) associated with protein
   model refinement and rebuilding.

 Before you start, copy your local version of the gmrp directory tree
   to your own area.  This contains all the files you need.  You will
   start working in the O directory, gmrp/o.

 For teaching exercises: to answer the questions, it may be useful to
   have a copy of the O manual and tutorial at hand.  The answers to most
   questions can be found in the literature references, program manuals,
   or by inspection (of the model, the density or some file).

 It may be handy to use a web-browser to consult the O manual and FAQ
   (  Manuals for the utility programs
   are available in HTML format as well (in Uppsala, via our homepage;
   elsewhere from the O ftp server, file "pub/gerard/html_manuals.dirtar.Z").
   Documentation for X-PLOR and CCP4 programs is also available on
   the WorldWide Web.

 While you work through the tutorial, you may also want to use the
   Good Model-building and Refinement forms for keeping notes (available
   as file "OMAC/").

 Rebuilding is a lot more fun if you play loud music on your personal stereo !

 Comments and suggestions about this tutorial can be E-mailed to
   gerard at


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