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. 25.2, pp. 729-730   | 1 | 2 |

Section 25.2.8.6. Making kinemages

D. C. Richardsons and J. S. Richardsons*

25.2.8.6. Making kinemages

| top | pdf |

Setting up a research kinemage is very simple, since most decisions will be made later, during its use. For instance, to make a contact-dot kinemage one would run REDUCE on the PDB-format coordinate file to add hydrogen atoms, then run the `lots' script in PREKIN (which produces vectors for the main chain, side chains, hydrogen atoms and non-water heterogens, balls for waters, and pointID's that include B factors), and then run PROBE, appending its contact-dot output to the kinemage file. In UNIX, these three steps can be combined in a command-line script.

Making a kinemage for teaching, publication, or distribution is a more iterative and deliberate process. Since MAGE and PREKIN continue to evolve, it is an advantage to use the latest version (Richardson Laboratory, 2000[link]). For a first look at what is in the PDB file, accept the default `backbone browser' option in PREKIN, which will produce a Cα backbone (or a virtual backbone for nucleic acids, as in Fig. 25.2.8.1[link]), disulfides and non-water heterogen groups for all subunits in the file and will automatically launch MAGE, where one can decide what else to add. In a second PREKIN run, one can choose from a menu of built-in scripts such as main chain plus hydrogen bonds, `lots', ribbons (as in Fig. 25.2.8.2[link]) or Cα's plus all side chains grouped and coloured by type. One can also ask for specified items in a `focus' around a chosen residue. Alternatively, in the `New Ranges' dialogue box, one can specify combinations of main chain, side chains, hydrogen bonds, hydrogen atoms, waters, non-water heterogens, balls, ribbons, rotatable or mutated side chains etc. for any set of residue ranges. Subunits (or models, if NMR) are chosen in a final dialogue. The resulting kinemage file will then be displayed and modified in MAGE.

On-screen editing of a kinemage in MAGE usually begins with setting up a few good views: rotate, pick centre, zoom and clip to optimize each one, and save it with `Keep Current View' on the Edit pull-down menu; it then shows up on the Views pull-down menu with the given label. Turning on `Change Color' (Edit menu) then picking any atom in an object allows selection of a new colour from the scrollable choices. Demo5_4b.kin shows the palette of colours with their names and gives some guidelines for choosing effective colours. Context is important for a kinemage (usually at least overall Cα's), but as much as possible should be deleted that is not directly relevant, while the features of current interest are emphasized (e.g. Fig. 25.2.8.1[link]). This selection process is like the simplification and emphasis needed for a good 2D illustration, but in this case it applies to the fully interactive 3D form. For a kinemage, however, it is both possible and advantageous to include some additional details for further exploration, controlled by a button which can start out turned off. For deleting things, `Prune' on the Edit menu activates four new buttons on the right-hand panel: `punch' removes the vectors on either side of a picked point, `prune' removes an entire connected line segment, `auger' removes everything within a marked circle on the screen and `undo p' recovers from a mistake, back for ten steps. If, for example, side chains are being shown in a focus around the active site, one could prune away those that don't interact at all, and then move the second-shell side chains to a separate list with the word `off' in its first line. `Text Editable' (Edit menu) enables writing explanations in the text and caption windows, while the graphics window is still active for reference. `Save As' (File menu) will save the whole edited kinemage file and reload to show the revised kinemage in its startup view. As well as a bitmap screen capture or files for rendering, a PostScript file can also be written to print out a 2D picture of the current graphics window, either in colour or `black on white'.

At this stage, a word processor can be used to look at the plain ASCII kinemage file, with its text, its views and the hierarchy of group, subgroup and list display objects in human-readable and clearly identified forms. Lists (e.g. @vectorlist {name}) can be of vectors, dots, labels, words, balls, spheres, triangles, or ribbons. Any part of the file can be edited, using its existing format as a guide or looking at another kinemage file that provides a desired template. Among the few operations that currently must be edited outside rather than inside MAGE are moving things between different lists or groups (for instance, setting up a new list of just active-site side chains in a different colour and controlled by their own button) and adding `master' buttons that control object display independent of the group heirarchy (e.g. side chains can be turned off and on together for all subunits or models if `master ={side ch}' is added to the first line of each of those lists). The kinemage should be saved without formatting, as a plain text file.

More complex modifications are possible in MAGE, using advanced on-screen editing and construction features from the Edit menu. `Draw new' activates tools that can add labels, draw hydrogen bonds (with shortened, unselectable lines) and make a variety of geometrical constructs by building out from the original atoms (e.g. add a Cβ to a Gly, or draw helix axes and measure their distance and angle). `Show Object Properties' lets one see, and edit, the names and parameters of the object hierarchy for any point picked, which allows renaming buttons, simplifying the button panel, adding animation, editing labels, or deleting entire display objects. `Remote Update', on the Tools menu, can call PREKIN to set up rotations for the last-picked side chain or a mutation of it, and can then call PROBE to update all-atom contacts interactively as the angles are changed. On the kinemage web site (Richardson Laboratory, 2000[link]), Demo5_4a.kin includes an introduction to the drawing tools and Demo5_4b.kin to the format and to editing. Make_kin.txt is a more complete tutorial on the process of constructing kinemages. Mage5_4.txt and Pkin5_4.txt document the features of the MAGE and PREKIN programs. File KinFmt54.txt (which also constitutes the MIME standard chemical/x-kinemage) is a formal description of the kinemage format for 3D display.

All in all, making a simple kinemage is trivial, but making really good ones for use by others is much like making a good web page. There are tools that make the individual steps easy, but one needs to exercise restraint to keep it simple enough to be both fast and comprehensible, patience to keep looking at the result and modifying it where needed, and judgment about both content and aesthetics.

References

Richardson Laboratory (2000). The Richardson's 3-D protein structure homepage. http://kinemage.biochem.duke.edu (or ftp://kinemage.biochem.duke.edu ).Google Scholar








































to end of page
to top of page