Sokolik, C.W., "KINEMAGE COOKBOOK: A TUTORIAL" gopher://gopher.prosci.uci.edu:70/00/Kinemage/Cook_Kin.txt A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. MAGE is a display program to view and explore kinemages; it presently runs on Macintosh, IBM-PC, and various UNIX computers,. Earlier versions of MAGE are described in the Richardson & Richardson article in the first issue of Protein Science (Jan. '92) and in TIBS vol. 19, pp.135-8 ('94). The official kinemage format description is available in file KinFmt42.txt, from the anonymous FTP site at suna.biochem.duke.edu/pub, as are updated program versions on the various computer platforms. A reader or student uses Mage to look at an already-existing kinemage file; to make a new kinemage of your own from PDB format coordinates, use the Prekin utility, also available from the above FTP site. This documentation file contains four sections: a) Brief instructions for using MAGE to look at kinemages; b) Features of MAGE; c) Changes since the last distributed version; d) Suggestions for trouble-shooting. * * * * * * * * * * * * * * * * a) Brief INSTRUCTIONS for looking at kinemages on the MAC: Double-click on one of the *.kin files that has a "helix-on-page" icon or on the MAGE application icon (or, drag the file icon and drop it on the program icon), and follow instructions as they appear. Read some or all of the scrollable text, click in the rear window to see the graphics, and rotate the image by dragging the mouse. Try the "Animate" button if there is one, select author-set views under the "Views" pulldown menu, and go to a new kinemage under the "Kinemage" pulldown. "Open File" under the "File" pulldown menu lets one open a new kinemage file, and "Quit" lets one exit from MAGE. (If you can't get the program running, please read the "Trouble-shooting" section below!) Brief INSTRUCTIONS for looking at kinemages on the PC: If you are still in DOS, then go to the diskette or appropriate directory and issue the command: "win mage_x_y.exe" ("x.y" is the version number). This will invoke windows and put you in MAGE, where you can select File from the menu. If already in windows, use the file manager to display the kinemage directory, then double-click on mage_x_y.exe. If you "asssociate" files ending in .kin with mage_x_y.exe, then double-clicking on the .kin file will invoke MAGE. If you have a MAGE entry in the Program Manager (a MAGE icon is provided for this) make sure it invokes the lastest version of MAGE. When running PC MAGE, proceed past the first banner window, read some or all of the scrollable text, click in the rear window to see the graphics, and rotate the image by dragging the mouse. Try the "Animate" button if there is one, select author-set views under the "Views" pulldown menu, and go to a new kinemage under the "Kinemage" pulldown. "Open File" under the "File" pulldown menu lets one open a new kinemage file, and "Quit" lets one exit from MAGE. (If you can't get the program running, please read the "Trouble-shooting" section below!) The Demo3_1a.kin file contains example kinemages and a tutorial for readers; file Demo3_1b.kin gives examples relevant for authors of kinemages, and Make_kin.tut is a more extensive authoring tutorial. All kinemages from the Protein Science journal can be found on the WorldWideWeb site at http://www.prosci.uci.edu. As always, old *.kin files are compatible with new program versions, but new files will not work well with older programs. Important: OLD VERSIONS OF MAGE SHOULD BE REMOVED COMPLETELY from your system, to avoid possible problems or confusion. (On the PC, you will also need to change the executable "associated" with the .kin extension.) Brief INSTRUCTIONS for looking at kinemages on UNIX: Download the program version for your system by FTP from suna.biochem.duke.edu/pub (all require X-Windows, and all but Linux need Motif), and put it somewhere accessible on the paths for your login. Run it by typing "Magexx filename.kin", or just "Magexx" and then open the file from inside Mage. If you want a simpler name for running Mage, then set up an alias. Once started, proceed as above. Looking at Kinemages over the WEB: There are kinemages on many Web sites, some of which are listed below. You can of course transfer those *.kin files to your own computer and then view them as above. However, if you want Mage to act as a built-in part of your browser, then merely follow the instructions in your Web browser to define Mage as a helper application, with ".kin" as its signal file extension. Kinemage Web sites: Protein Science, http://www.prosci.uci.edu, /Kinemages or /ProTeach Structure: PDB (Protein Data Bank): http://www.pdb.bnl.gov/Kinemage NDB (Nucleic Acid Databank): http://ndbserver.rutgers.edu Entrez: http://www3.ncbi.nlm.gov/Entrez VSNS-PPS ("virtual course"): http://seqnet.dl.ac.uk:8000/vsns-pps * * * * * * * * * * * * * * * * b) FEATURES of MAGE There are versions of MAGE for IBMpc-type, Macintosh, and UNIX computers. Although copying, loading, and starting them depends on the operating system (see part a), once inside MAGE the versions are nearly indistinguishable. [In the initial banner window there is a choice called "student mode". Although seldom necessary since Mage is very simple to use, it provides a stripped-down version for the computer-shy, without some of the more complex features: file writeout, "kluges", and "pickshow" editing.] The main feature of MAGE is interactive rotations to help visualize objects in 3ĞD. Holding the mouse button down while the cursor arrow is in the graphics window will rotate the kinemage as the mouse is moved. Starting this in the lower 5/6 of the screen gives combined rotations around the horizontal (x) and vertical (y) axes. Starting with the cursor arrow in the top 1/6 of the screen gives rotation in the plane of the screen around the third (z) axis. (Notice that the cursor looks slightly different when you hold down the mouse in those two areas.) Another major feature is that the kinemage file which specifies the display list is readable and editable plain ascii text, so in addition to the on-screen graphics editing features, authors can iteratively construct and modify kinemages using their favorite wordprocessor (save as a plain "text" file!). PREKIN is a utility program to do an initial construction of a kinemage from an atomic coordinate file in Brookhaven Protein Data Bank format. However, MAGE can display anything that can be specified as lines, dots, balls, and labels. Each point, be it atom, label, dot, ball, etc., can be picked by clicking the mouse button when the arrow cursor is on the point. An identifying string for that point, specified by the author (usually the atom name), is displayed on the screen, and the distance from the previously picked point is shown. The exception is "unpickable points", which are specified in the kinemage file by a "U" preceding the point triple. These are used primarily for the ends of shortened H-bonds or for the ends of 3-D crosses used as atom markers. Since such positions are not atom locations, it is better that they not be pickable for distance measurements. If you do need to pick one, however, that can be done by turning on the "superpick" function on the "Edit" menu. The text window contains the author's explanation of the kinemages in this file; scroll down to read it, or click on any of the windows to bring them forward. At the top of the text window there is usually a title and author and a Table of Contents with a one-line description of what is in each kinemage. If you find a piece of the text set off with *{ }*, then clicking within that region will either take you to a particular kinemage and view in the graphics window, if that was the type of specification, or if it was a question then the click will bring up a dialog box in which to answer the question, including using previously-picked points or distances from the graphics window if appropriate. After answering the questions, you can write out a file with all the questions and answers (under "File"). MAGE displays to the right side of the graphics area a set of labeled check-buttons to select what graphics objects will actually be displayed. These follow a three-tiered hierachical organization, specified by the author with keywords @group; @subgroup; and @vectorlist, @dotlist, @labellist, @balllist, or @wordlist. In addition there are "master" buttons, which can control any number of groups, subgroups, and lists thus providing a way of grouping display-objects that is orthogonal to the group-subgroup-list heirarchy. An author sets up master buttons by adding the parameter "master= {masterbuttonname}" to the top line of ,e.g., each relevant vectorlist; MAGE makes a master button for each different masterbuttonname. They appear after all the group buttons, and from the reader's point of view, they act just like any other button. (When master buttons are used, typically the individual list buttons are supressed by making their groups dominant.) If there is more than one group with the parameter "animate" (or "2animate") then an "animate" ("2animate" ) button is created that steps in turn through all such marked groups, flagged with an * (%). An "ANIMATE" button should always be tried if it is present; alternatively, type 'a' (or 'b') on the keyboard. To move backwards in an animation sequence, type 'A' (shift, a) or hold down the shift key while clicking the animate button. Animations can show conformational changes, build up objects cumulatively in steps, switch among color-schemes, show a sequence of logical steps, or provide a tour where viewpoint as well as object selection is changed between steps. Changing viewpoint is specified by adding a parameter "moview= n" to the line that specifies the animation, which will then use View n. Three buttons standardly appear below the graphics objects buttons: one to toggle on and off markers that show the last two pick-points; one to turn on or off pickcentering; and another to toggle the z-clip function off or on. When the "pickcenter" button is on, the image will be recentered around each new point clicked with the mouse. To avoid unintended jumps, leave pickcenter off except when you are actively using it. (Other buttons appear in that region when additional functions are enabled.) Three vertical scrollbars to the right of the button area of the graphics window control the zoom scale factor, the z-slab thickness, and the z-translation. The defaults are such that in most cases all you need do is change the zoom factor. The scrollbars work like others on the Mac or in Windows: either click on the arrows for small changes, or click or hold in the open part of the bar for larger changes, or drag the slider. The value of the parameter is displayed at the top of the scrollbar; moving the slider downward increases the parameter. If the "zclip" button is turned off, then the z-slab is inoperative and the entire depth of the object will be displayed, although depth cuing is still relative to the clipping planes. The graphics window can be expanded to better fill the screen: either click on the expansion symbol at the right end of its top bar (Mac), or else move the window left and then drag out the lower right corner of the window. Pull-down menus from the top menu-bar invoke additional features built into MAGE; some of these can also be invoked by keywords in the display list (kinemage) file or by keyboard commands. Some menu features result in additional check-buttons. Some menu choices deal with mechanics, such as the "Show text", "Show caption", and "Show graphics" items under the "Window" menu which can be used to bring front any of these windows if they get lost behind the others. "Next" and "Choose" under the "KINEMAGE" menu let one progress through the individual kinemages of a particular kinemage file. Authors can specify up to nine different orientations of a kinemage (using the keywords @viewid, @zoom, @matrix, @2matrix, @2center, etc.); these show up as View1, View2, View3, etc. under the "VIEWS" pulldown menu. A checkmark appears next to the one you last chose, and there can be a short label for each view. Also, the reader can specify a view (with the "set reader view" command on the "Other" menu) and return to it at any time during a session by choosing "Reader's view" on the VIEWS menu. These views store the values of zoom, center, slab, etc. as well as orientation. The "Update view" function, on the "Edit" menu, sets the current orientation matrix and values of zoom, center, and slab to whichever numbered view is specified, and lets you give it a label (viewID). "Stereo on" from the "Other" pulldown menu, invokes side-by-side stereo; alternatively, type 's' on the keyboard. This divides the graphics window in half vertically, with left and right images differing by a 6 degree rotation. Such side-by-side stereo can be used with a suitable viewer, or else just by relaxing your eyes to focus toward infinity, letting the two images drift together until they overlap, and then focusing on the fused image to see 3-D. Each half-screen is clipped at the centerline as well as the edges, so that the stereo can be used with large, or even zoomed, images. The 200-pixel separation between left and right halves varies in absolute distance on different monitors, but in most cases it is reasonably close to correct eye separation (you may need to sit further back from a large screen). If you wish to experiment, the stereo angle and separation can be altered by invoking "stereo angle" on the "Kludges" submenu. For example, if the depth looks exaggerated to you, then make the stereo angle somewhat smaller. (Switching from wall-eye to cross-eye stereo is much more conveniently done by typing 'c' on the keyboard, which takes the negative of the current stereo angle.) Such changes remain in effect until the program is quit and restarted. "Stereo on" is reset off when a new kinemage is loaded, unless "s" was typed on the keyboard, which invokes a "keepstereo" mode. The split screen is sometimes used for a side-by-side comparison of two different things, rather than for stereo. This is specified by an author using the keyword @compare and otherwise setting up as for an animation. A reader can also change mode between animation and side-by-side comparison, by enabling or disenabling "compare" on the Kludges submenu (note that stereo and compare are incompatible, so when one is on the other will be grayed out). Rotation will move both objects in the same way, keeping them lined up. Toggles controlled by specific keys on the keyboard make it possible to invoke thinline ("t", for faster rotation on the PC), to turn on stereo ("s"), to change between normal and cross-eye stereo ("c"), or to turn on perspective ("p"). In each case the option will stay in force between kinemages, for an entire MAGE session, but can be turned off at any time by hitting the same key again. If you forget which key controls what, look it up under "secret spells" in "Help" on the "Other" pulldown menu. Menu item "onewidth", on the "Options" menu, (keyword @onewidth in a kinemage file) over-rides additional depth-cuing by line thickness as well as color saturation for a particular kinemage, and "thinline" (@thinline) makes the lines very thin, which is useful for multiple superimposed structures or to speed up rotation. "Perspective" (@perspective) is useful if the object is regular enough to have recognizable size depth cues or foreshortened straight lines, but the default of non-perspective, orthographic projection seems to be best for molecules. "white bkg", with a different color palette on a white field, is useful for certain kinemages such as 3-D graphs; "B&W monitor" simulates the default mode for black and white monitors, to make black-and-white illustrations by writing a Postscript file (see below) or by bitmap screen capture (using one of the many inexpensive utilities available, such as SnapJot). "Measures", selected under the "Other" menu, is a natural extension of the point-ID and distance functions to include angles and dihedrals, also reported on the "information line" at the bottom of the graphics window. Reported values are the point-ID for the last point picked, the distance between the last two points, the angle defined by the last three points, and the dihedral defined by the last four points. It is possible, therefore, to pick successive points along the polypeptide backbone and see successively the values of phi, psi, and omega dihedral angles. (Note that the dihedral refers to the central bond of the 4 points, so that it seems to lag behind where you are currently picking.) The measure function displays white lines between the points it is currently using, and displays red dots that are the averages of the last two, the last three, and the last four points picked. These points can themselves be picked, so that you can use them to recenter the image, to measure distances, or as the ends of drawn lines (you probably want to turn off the "measures" button before using those points for another purpose). For example, you can add a helix axis to the display by invoking measures and picking 4 Calpha atoms at one end of the helix, turning the measures button off and drawline on (with a "shorten line" value of, say, -2.5 A) and picking the 4-point average dot; then turn the drawline button off and measures back on and repeat the process at the other end of the helix. Such new lines may be written out to a file (see paragraph below) and then pasted into the kinemage file (renamed and recolored) to become a permanent part of it. The "find" function under the "Other" pulldown menu lets you search for particular strings in the pointID's, so for instance you could locate the point whose ID contained both "ca" and "195". "Find" works just like a mouse-click, so depending on what functions are currently enabled, it could put a marker on the point, recenter on it, label it, draw a line to it, etc. "Change color" is the most frequently used function on the "Edit" menu. When its button is turned on, a pick brings up a scrollable list of colors for resetting the color of the picked display object. You can see the effect of the new color on screen before accepting it. "Draw new", under the "Edit" pulldown menu, brings up a dialog box that lets you set various options and enable 4 different tools for adding new lines or labels to the kinemage (and then later writing them out). Buttons will be added to the panel for all 4 tools, only one of which can be turned on at a time. When the drawline tool is invoked, MAGE will add a green line to the display between each alternate pair of points picked. They can be erased, one at a time in reverse order, by clicking on "eraselast" in the button panel (this applies to objects drawn by all 4 tools). The "drawline" button on the button panel will enable or disenable the drawing of new lines without effecting previous lines (in order to use mouse-clicks for other purposes). The lines can be drawn either shorter or longer than the distance between picked points, according to the value chosen in the dialog box. For hydrogen bonds, it is suggested to shorten them by .7 Angstroms, and to check the "unpickable" box. To lengthen lines (e.g., for a rotation axis or a helix axis), give a negative "shorten line" value. The "construction" tool works like an inverse "measures": you pick 3 points in succession and are then given a dialog box in which to specify the length, angle, and dihedral for a new line to a 4th point. You can copy an existing piece of geometry (say, to add a Cbeta to a Gly), by measuring it and then turning on "Construct" to reproduce it at the new position. The "dragline" tool lets you click and drag from a pre-existing point, moving in the plane of the screen (for example, to place a label out away from any atom). If the "Labels" button is on, then the pointID of any point clicked on will be displayed on the screen at that point. The contents of such a label can later be edited, either in "pickshow" (see below) or in the file itself. The total set of drawn lines and/or labels can be written out using the "draw_new parts" choice under "Write" of the "File" pulldown menu. If "draw new" is turned off from the edit menu, then all drawn lines or labels will be removed. The "Edit" menu has several other functions that allow on-screen graphics editing of the kinemage. "Prune" turns on two buttons marked 'punch' and 'prune', which allow you respectively to delete the two vectors attached to a picked point, or to delete all vectors in the same P,L,L,L sequence as the picked point. There is also an 'undo p' button which works for about 10 steps back. 'Pickshow' lets you see and edit almost all characteristics of a display object. The most frequently useful are to edit the button names, delete entire display objects, or set "dominant' parameters that hide buttons for lower subgroups or lists. The contents of a label can be edited by this mechanism (you will usually need to turn off the molecule so that the pick chooses the label rather than an atom). The "Kluges" submenu of "Other" includes a variety of features that are highly specialized, esoteric, and/or in testing. For instance, "Graphics Fonts" lets you increase the size of characters for the on-screen labels or information line, which is very valuable if you want the audience to read numbers when you measure distances in an interactive lecture. If "XYZ point" is on, the coordinates of each point picked are written at the top of the screen. "Gnomon" displays a 3D cursor at the current center, with axes along the original coordinate axes. "Count" will say how many drawn items are currently displayed, out of how many total in this kinemage. "Flatland" changes mouse-dragging into a 2-D scrolling motion. "Kaleidoscope" is purely for diversion - it turns off the screen-refresh, so that rotation smears the objects and colors across the image. Mage can rotate around as many as 10 bonds, if a rotatable sidechain (with or without mutation) has been specified in Prekin (see tutorial file Make_kin.tut for an example of how to do this). The rotations are controlled by an additional panel of scrollbars, with starting and current angle values shown, and the rotated parts can be written out either in kinemage or in PDB format. After editing a kinemage to your satisfaction, it can be written out (just one kinemage plus its caption, or including text if it's Kin.1) with the "modified kin" choice of "Write" on the "File" pulldown menu. Other write functions allow writing out just part of a kinemage (such as one view, or the drawnew objects). A 2-D image of the graphics window can be written out as a Postscript-format file with 'write postscript' under the "File" menu. It produces a generic Postscript file readable by many but not all programs; on the Mac, for instance, it can be downloaded to a laser printer by the Laserwriter Font Utility which comes on the system disks for System 7, or to a non-laser printer by programs like Freedom of Press. * * * * * * * * * * * * * * * * c) CHANGES since the last distributed version: UNIX versions of Mage are now available, for SGI, ESV, Sun Solaris, and Linux (by anonymous FTP from suna.biochem.duke.edu/pub). The "generic" UNIX version can be made to run on most machines with X-Windows and Motif. Program changes since Mage 3.2 are mostly internal, to make the UNIX, PC, and Mac versions share as much code as possible. The most visible new feature is a clearer menu organization, grouping all editing functions (including a simpler and more accessible "change color"), and with all types of writeout grouped under the file menu. The help functions have been expanded somewhat, with a new "Help" item on the "Other" pulldown menu, plus the "About x" entries on most menus. The initial banner box now includes a "student" mode option for the computer-shy, which runs a stripped-down version without some of the more complex features: file writeouts, the "kluges" submenu, and the "pickshow" and "superpick" editing functions. There is no longer an explicit atom limit; Mage now reallocates storage dynamically if the kinemage is large. If it cannot grab enough, however, then one must quit and increase the available program size (see part d). It is now possible to move backwards in an animation sequence, by typing 'A' or holding down the shift key when clicking the animate button. PointIDs can now be 20 characters long, and a kinemage with overlength ones produces a single error message but can still be viewed. The keyword @flat makes mouse-dragging control a 2-D scrolling motion rather than the usual 3-D rotation, for 2D kinemages such as NMR spectra, annotated sequence layouts, etc. The parameter "static" makes that display object immune to rotation, scaling, or centering operations - for use as an enclosing box, a background, an "inset" reference diagram whose parts can be turned on in synchrony with an animation sequence, etc. * * * * * * * * * * * * * * * * d) The following are suggestions for TROUBLE-SHOOTING problems with kinemages: 1) MAGE VERSIONS - Are you using an up-to-date version of the program? MAGE has changed substantially over the past several years, including correction of errors. Any older versions should preferably be TOTALLY REMOVED from your system, since they can be invoked unintentionally when you double-click on a *.kin file. To tell which version is running, check the date and version number in the banner window that first comes up when you start MAGE. MAGE should run on any Macintosh with any system version (including the PowerMac), but will run on a PC only with Windows version 3.1 or later, and on UNIX only with X-Windows and Motif. When you update versions on the PC, remember to "associate" the new application with the *.kin file extension. The most reliable source of updated program versions is the anonymous FTP site maintained by David Richardson at suna.biochem.duke.edu/pub, which is also mirrored on the PDB Web site at http://www.pdb.bnl.gov/Kinemage. 2) COLORS - Is your monitor set to show 256 colors? MAGE works best with 256 colors, no more and no less. On the Mac, if your monitor is set to 16 colors, 16 grays, or 256 grays MAGE will produce a display depth-cued in gray shades, and for any fewer bits it will be limited to pure black and white. If it is set to more than 256 colors, then depending on the program version you will either get an error message, or else Mage will change the color setting itself and restore it upon exit (4.4 or later). To change the color settings of your monitor (Mac), pull down the apple at left of menubar and release at "control panel." In the box that comes up, click on the "monitors" icon. Select "colors" rather than "grays," and "256" rather than a smaller or larger number. Put the box away by clicking in the square at its upper left. 3) RUNNING MAGE - If you have any problems, the most reliable way of viewing a *.kin file is to drag and drop it onto the program icon (for Mac System 7) or to double-click on the MAGE icon (the hand holding out a helix) and then open the file from inside the program. The *.kin files as distributed (with a helix-on-page icon) will launch MAGE and read themselves in if you double-click them, but they may launch another version of MAGE if there is more than one present on your system. If you are sure you have no other program versions, then it is fine to double-click the *.kin files. On the PC you do not need to worry about program versions if you have associated the right one with the *.kin extension. 4) MEMORY - If your computer is having memory problems, first make sure no other applications are running. MAGE needs 950K of application memory to run in color, and about 400K in black-and-white. On a black-and-white Macintosh system with limited memory, select the MAGE icon, choose "Get Info" under the File menu, and change the minimum memory size to match available memory. Restarting the computer helps under some circumstances. If you are using Mac System 6, it is worth trying to run under Finder rather than Multi-Finder. For large kinemages (over 3500 atoms or points), Mage now reallocates memory dynamically. If it cannot manage to get enough, it will give an error message. You then need to quit, use "Get Info" to increase the preferred program memory, and try again. If you use the graphics window-expansion button (upper right corner) on a large screen but the window fails to expand to fill the screen, that means insufficient program memory is available. Fix as above. 5) MULTI-TASKING - Although MAGE is very user-friendly, it does not like other programs. Current versions of MAGE may not work if another program is running, including "Inits" or "Applets" that are actively running in the background. Crashes can therefore be caused by incompatibilities with some "Init" files on the Mac or "Applets" on the PC. To check out that possibility for the Mac, try restarting with the shift key held down (to disable all inits) and try MAGE again. If you are using Mage on a machine where you standardly need more than 256 colors for other programs, then you should be sure to use Mage 4.4 or later (Mac) which can internally change and restore the color setting. 6) ICONS A *.kin file created by an older PREKIN is initially a plain text file (icon = blank page on the Mac) that won't launch any application (newer Prekins produce files with Mage icons), and if you edit a *.kin file, it will then be "owned" by your word processor (however, remember to save it as a text file, NOT a formatted word-processor file). The ownership is not a problem, since any of these plain text file types can be opened from inside MAGE, or dragged and dropped. [For Mac aficionados, it is possible to produce the helix-on-page icon for a *.kin file by using ResEdit or FileTyper to modify the "Creator" field to say "MAGE".] If the *.kin files on the distribution diskette do not show the helix-on-page icon, then you probably have, or once had, a very old version of MAGE on your system. Throw away all old copies of MAGE and rebuild your desktop by holding down both the option and the apple keys while restarting the computer. Double-clicking on the *.txt or *.tut files on a Mac will launch TeachText or SimpleText if they are on your system; alternatively such files can be opened from some other word processor or by MAGE. Files longer than 32K show blank-page icons on a Mac and cannot be handled by TeachText or inside MAGE; use a word processor to look at them. On the PC, get the MAGE.ICO (and PREKIN.ICO if using Prekin) icon files as well as the *.EXE application file. 7) MISSING WINDOWS - If you lose the text window behind an expanded graphics window, bring it forward with "Show text" under "Windows" on the menubar. 8) WILD LINES ON DISPLAY - If you have edited a *.kin file and it is now behaving strangely, that is most likely to be either a) because you saved it as a word-processor rather than plain text file (just bring it up again and re-save it); or b) that the point triples are out of register because you either omitted a curly bracket or are missing a delimiter (blank, comma, or carriage return) between a number and a curly bracket or between two numbers. Click on the ends of any strange lines in the display to get their pointID's and/or identify their set by color or by turning things on and off, and then look for problems in that part of the file. Turning on "XYZ point" on the "Kluges" submenu will help identify lines. Wild lines could perhaps be caused by a bad copy of the file. 9) BALL&STICKs look odd - If the vectors are not truncated correctly at the balls, it means they precede the balls in your kinemage file. Move the balllist to be in the same group but BEFORE the relevant vectorlists. For more information see other Kinemage Cookbooks: http://www.prosci.uci.edu/kinemages/Cook_kin.txt http://www.prosci.biomol.uci.edu/kinemages/Cook_Kin.txt