International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 17.1, pp. 354-355

Section 17.1.3.  RAVE

G. J. Kleywegt,a J.-Y. Zou,a M. Kjeldgaardb and T. A. Jonesa*

aDepartment of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden, and  bInstitute of Molecular and Structural Biology, University of Aarhus, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark
Correspondence e-mail:  alwyn@xray.bmc.uu.se

17.1.3. RAVE

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RAVE is a suite of programs for electron-density map improvement and analysis, with a strong focus on averaging techniques (Kleywegt & Read, 1997[link]). It is the successor of an older package (`A') (Jones, 1992[link]), and at present it contains tools for single and multiple crystal form, single- and multiple-domain NCS averaging of electron-density maps, and the detection of structural units in such maps. The package works in conjunction with the CCP4 suite of programs (Collaborative Computational Project, Number 4, 1994[link]).

RAVE contains the following programs for density averaging involving one crystal form:

  • (1) AVE (Jones, 1992[link]). This program carries out the averaging step and the expansion step (in which the averaged density is projected back into the entire unit cell or asymmetric unit).

  • (2) COMA (Kleywegt & Jones, 1999[link]). This program uses the algorithm of Read (Vellieux et al., 1995[link]) to calculate local density correlation maps that can be used to delineate masks (molecular envelopes). It can also be used to validate structural differences between NCS-related molecules (Kleywegt, 1999b[link]).

  • (3) IMP (Jones, 1992[link]). This program can be used to optimize NCS operators relating two copies of a molecule (or domain) inside the same cell. The program adjusts the initial operator (e.g. obtained from heavy-atom positions) so as to maximize the correlation coefficient between the density inside the envelope and its NCS-related counterpart. The procedure can be controlled by the user or run in automatic mode, which usually gives satisfactory results.

  • (4) NCS6D. This program can be used to find NCS operators in cases where it is difficult to obtain them by other means. The program uses a set of BONES atoms (or a PDB file) and, for a large number of combinations of rotations and translations, calculates the correlation coefficient between the density around the atoms and that obtained after application of the rotation and translation. This approach was used, for instance, to find the operators in the case of maltoporin (Schirmer et al., 1995[link]).

  • (5) COMDEM. If a molecule contains multiple domains that have different NCS relationships, the individual domain densities can be averaged with AVE and subsequently combined with this program. AVE can then be used to expand the density back into the unit cell or asymmetric unit.

  • (6) SPANCSI. This program is useful when NCS-related molecules are known or suspected to have very different average temperature factors. One option is to analyse the similarities between NCS-related copies of the molecular density (variance, correlation coefficient, R factor). In addition, the program can carry out electron-density averaging and expansion, in which each copy of the density is scaled by its variance.

RAVE also contains tools for averaging between different crystal forms, namely:

  • (1) MASKIT (Kleywegt & Jones, 1999[link]). This program calculates a local density correlation map from the density of two different crystals or crystal forms, using Read's algorithm (Vellieux et al., 1995[link]). This program can also be used to validate structural differences between related molecules, for which experimental electron density is available (Kleywegt, 1999b[link]).

  • (2) MAVE. This program does the (skew) density averaging and expansion steps, but now separately because the density of the various crystal forms has to be averaged as well. This program also contains an option to improve operators that relate the position and orientation of the molecular envelope (mask) in one crystal form with those in other crystal forms.

  • (3) COMDEM. This program combines the individual (possibly averaged) densities from various crystal forms. The densities are scaled according to the number of molecules whose (averaged) density they represent as well as according to their variance.

  • (4) CRAVE. Since the book-keeping for multiple-crystal-form averaging can become rather complicated, this program can be used to generate one large C-shell script that will execute a user-defined number of cycles of multiple-crystal-form averaging.

More recently, RAVE has been expanded to include tools that can be of use in map interpretation:

  • (1) ESSENS (Kleywegt & Jones, 1997a[link]). This program takes a (rigid) structural template (e.g. a penta-alanine helix or strand, or a ligand) and calculates how well it fits the density by doing an exhaustive rotational search for every grid point in the map. The resulting score map will reveal places in the map where the centre of gravity of the template fits the density well. The method is very effective for detecting secondary-structure elements (prior to human map interpretation), as discussed by Kleywegt & Jones (1997a[link]). The ESSENS algorithm has also been implemented within O (Jones & Kleywegt, 2001[link]).

  • (2) SOLEX. This program can be used to extract the best-fitting positions and orientations of a structural template as found in an ESSENS calculation. If the search used a template in helix or strand conformation, the program can also be used to combine short stretches of helix and strand into longer units. The results (helices and/or strands of unknown connectivity and uncertain directionality) can be fed into another program, DEJAVU (Kleywegt & Jones, 1994b,[link] 1997b[link]) (see below), to check if they are similar to (a part of) another protein whose structure is known (Kleywegt & Jones, 1994b[link]).

Finally, RAVE also contains three utility programs that can be used to manipulate three essential data structures encountered in averaging, map interpretation and refinement:

  • (1) MAMA (Kleywegt & Jones, 1994b[link], 1999[link]). This program is used to generate, analyse and manipulate masks (molecular envelopes). It contains many of the tools described earlier by Jones (1992)[link], but many new features have been added to it since. Masks can be generated from scratch, using a PDB file or BONES atoms, by `recycling' another mask (e.g. from a different crystal form), or by combining several older masks. The quality of masks can be improved by filling voids, removing unconnected `droplets', smoothing the surface, trimming regions that give rise to overlap through (non-)crystallographic symmetry and checking that all atoms in a model are covered by the mask (e.g. after changes or extensions to a model have been made).

  • (2) MAPMAN (Kleywegt & Jones, 1996a[link]). This program was written for format conversion, analysis and manipulation of electron-density maps. Maps can be read and written in a variety of formats, including those used by O. Maps can be combined, scaled, peak-picked and subjected to `digital image filters' (Kleywegt & Jones, 1997a[link]). Several older stand-alone programs have been incorporated into MAPMAN, such as MAPPAGE and BONES (Jones & Thirup, 1986[link]; the program previously used to skeletonize electron density for use with Frodo or O). Many statistics and types of histograms and plots (e.g. slices, or 2D and 1D projections) can be calculated or generated.

  • (3) DATAMAN (Kleywegt & Jones, 1996a[link]). This program is used for simple format conversion, analysis and manipulation of reflection data sets [consisting of Miller indices, F, σ(F), and possibly a cross-validation flag]. Data can be sorted, Laue symmetry can be applied, and data can be scaled by a temperature and a scale factor, re-indexed, and reduced in special cases where higher symmetry is present or suspected. The program contains a wide range of options to select `test set' reflections that are to be set aside for cross-validation purposes (Brünger, 1992a[link]; Kleywegt & Brünger, 1996[link]). Many statistics and types of histograms and plots can be calculated or generated.

References

Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760–763.Google Scholar
Brünger, A. T. (1992a). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature (London), 355, 472–475.Google Scholar
Jones, T. A. (1992). A, yaap, asap, @#*? A set of averaging programs. In Molecular replacement, edited by E. J. Dodson, S. Glover & W. Wolf, pp. 91–105. Warrington: Daresbury Laboratory.Google Scholar
Jones, T. A. & Kleywegt, G. J. (2001). New tools for the interpretation of macromolecular electron-density maps. In preparation.Google Scholar
Jones, T. A. & Thirup, S. (1986). Using known substructures in protein model building and crystallography. EMBO J. 5, 819–822.Google Scholar
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Kleywegt, G. J. & Jones, T. A. (1994a). Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Cryst. D50, 178–185.Google Scholar
Kleywegt, G. J. & Jones, T. A. (1996a). xdlMAPMAN and xdlDATAMAN – programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Cryst. D52, 826–828.Google Scholar
Kleywegt, G. J. & Jones, T. A. (1997a). Template convolution to enhance or detect structural features in macromolecular electron-density maps. Acta Cryst. D53, 179–185.Google Scholar
Kleywegt, G. J. & Jones, T. A. (1997b). Detecting folding motifs and similarities in protein structures. Methods Enzymol. 277, 525–545.Google Scholar
Kleywegt, G. J. & Jones, T. A. (1999). Software for handling macromolecular envelopes. Acta Cryst. D55, 941–944.Google Scholar
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