NEWS FROM THE UPPSALA SOFTWARE FACTORY - 7
Taking the fun out of map interpretation ...
Gerard J. Kleywegt & T. Alwyn Jones
Department of Molecular Biology
Biomedical Centre, Uppsala University
Uppsala - Sweden
Interpretation of experimental electron-density maps has traditionally been a difficult,
time-consuming, yet also fun and exciting step in the structure-determination process.
It is one of the few activities for which (successful) black boxes have not yet been
We have recently described a method to detect rigid structural entities in electron-density
maps [1, 2], and implemented this in a program called ESSENS , which is distributed
as part of the RAVE package . Briefly, this program reads a map and a structural fragment,
oes a complete rotation of the fragment for every grid point in
the map, and for each position and orientation calculates how well the fragment fits
the local density (the "score"). When the calculations are finished, the scores
are written out as a new map, which can be contoured in O . By using a penta-alanine
fragment in either ideal alpha-helical or ideal beta-strand conformation as the template,
the result is a new map which shows how well a helix or strand fits at each point
in the map. Examples of the application of this technique to two structures are discussed
in , and figures of the "helix and strand maps" are also available on the Web
. This technique, simple (and CPU-time consuming) as it is, turns out to be very
powerful. First, if the score map reveals helices and strands, the model-building
process is greatly facilitated. Second, if the score map is featureless, this may
well indicate that the phases are not good enough, and that the crystallographer
is probably better off spending some more time on collecting more derivative data than on staring
at an uninterpretable map.
The previous paragraph basically describes the state of the program at the time when
the paper [1, 2] was submitted. Since then, a number of improvements have been made.
First, Morten Kjeldgaard suggested a modification of the algorithm which essentially
imprints and image of the helix or strand in the score map. The effect of this
is that the map becomes much clearer and easier to interpret. In the original implementation,
the image of a strand or helix looked essentially like a C-alpha or main-chain trace with
little detail. In the new version, the image includes all atoms of the
poly-alanine fragment, and in particular the visibility of the C-beta atoms is a
major improvement (which, in the case of helices, makes it very easy to deduce their
directionality). Initially, Morten's modification was applied for every orientation at every
grid point, which made the method ~2 times slower than the original one. However,
it can easily be applied a posteriori
, which means that in a single run of the program one obtains both the original score
map and the map which results from Morten's modification. This is how the method
is currently implemented in ESSENS. The map resulting from Morten's modification
is called the display map, since it is the most appealing for contouring purposes.
A shortcoming of the original program was that, although the output map showed where
the structural fragment fitted the map, the information about the best-fitting orientation
was completely lost. This has recently been changed, by storing the best set of rotation
angles for every grid point (encoded as a single integer number), and writing
these out to a file. A new program, SOLEX  (for SOLution EXtractor) was written
which reads the score map, the rotation file and the structural fragment, and extracts the
top solutions, writing them to a new PDB-formatted file. This PDB file can
be read into O again, and the fragments of strand or helix can be used in the model-building
process. In addition, specifically for helices and strands, an (experimental !) option is
available which will attempt to "connect the dots", i.e.
to merge bits of strand or helix which lie close to one another and are more or less
parallel, in order to build up longer secondary structure elements. At present,
the algorithm appears to be working reasonably well, except that the directionality
is sometimes wrong, so the crystallographer must be alert.
IF THE FOLD IS OLD ...
The secondary structure elements that are found by SOLEX are also written to a file
which can used as input to DEJAVU . DEJAVU is a program that looks for fold similarities
between a structure and a large database of structures derived from the PDB. At the 1994
CCP4 study weekend, we demonstrated the use of DEJAVU in finding proteins
with similar folds using only Bones-derived "secondary structure elements" (in effect,
these are simply guesses of the beginning and end coordinates of helices and strands),
even when the directionality of the helices and strands is unknown (or uncertain).
Similarly, the files now produces by SOLEX can be fed into DEJAVU, and the program
will attempt to find other proteins with a similar (partial) fold. In our standard
test case (P2 myelin protein), this works surprisingly well. SOLEX finds eight beta-strands,
and when DEJAVU is asked to look for similar proteins which have at least six strands
in common with our "unknown" structure (ignoring directionality), the program comes up
with four correct hits (including P2 myelin protein itself), and no false
hits, albeit that the orientation of one of the hits is wrong. Nevertheless, if
this were a real case, the tracing problem would essentially be solved, in that the
coordinates of one of the DEJAVU hits could be "stolen" to jump start the model-building
ESSENS and SOLEX also have other applications, for example in real-space, phased molecular
replacement calculations (although in this case reciprocal-space methods are probably
to be preferred for reasons of speed). This method was used in the structure determination
of an acetylcholinesterase/fasciculin complex . The acetylcholinesterase
molecule was easily found using standard molecular replacement techniques. However,
positioning the fasciculin molecule in a map phased on acetylcholinesterase was difficult.
ESSENS was used to verify the manually obtained solution (which was correct),
by using a truncated poly-alanine model of fasciculin as the search fragment (see
, , and  for details). For this type of calculation, the ability to extract any
number of solutions conveniently with SOLEX is obviously important.
Finally, we have experimented with other types of template, such as a di-alanine,
a tryptophan ring, etc.
, with varying results. There is no inherent limitation on the type of structural
fragment that is used as a template other than that it must be (assumed to be) rigid,
not contain any free conformational torsion angles. Hence, the method should also
work very well when searching for nucleic acids, sugar rings, many ligands, structural
, hairpin turns) or even structural domains.
The RAVE package (which includes ESSENS, SOLEX and many other programs) is available
to academic users free of charge (from the O ftp server). For more information
about RAVE, contact GJK (firstname.lastname@example.org). For more information about O, contact
-  Kleywegt, G.J. and Jones, T.A. (1997). Acta Cryst. D53, in the press.
-  A preprint of reference  is no longer available from our Web site
since this paper has now been published
-  The manual for this program is available at URL:
-  Kleywegt, G.J. and Jones, T.A. (1994). In "From First Map to Final Model
", pp. 59-66, CCP4 Proceedings.
-  Jones, T.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard, M. (1991). Acta Cryst.
-  The manual for this program is available at URL:
-  Harel, M., Kleywegt, G.J., Ravelli, R.B.G., Silman, I. and Sussman, J.L. (1995).
Structure 3, 1355-1366.
The Uppsala Software Factory now has its own home page on the World Wide Web, providing
access to many resources and services in Uppsala, including:
The URL is: http://xray.bmc.uu.se/usf/
- manuals for, and information about Gerard's programs
- previous publications in this Newsletter
- some preprints
- educational material (O, model building, and refinement and rebuilding)
- several resources pertaining to hetero-compounds, and the generation of dictionaries
for such compounds for both O and X-PLOR
- our local (non-serious !) Newsletter, DOMBO (to entertain you while you wait for
your ESSENS job to finish)
Latest update at 12 February, 1998.