.\" @(#)mindtool.l 2.4; .TH MindTool 1L "2 June 1990" "Local" "LOCAL COMMANDS" .SH NAME MindTool \- Manipulate molecules and atoms for display and analysis. .SH SYNOPSIS .br .B mindtool .I [ -i icon ] [ filename ] .SH DESCRIPTION .LP .I MindTool is a tool provided for the interactive graphic manipulation of molecules and atoms. Currently, up to 10,000 atoms may be input. .I MindTool has several subwindows: .TP 3 + A large drawing area or canvas for molecular display (on the left). .TP + A control panel at the upper right with buttons corresponding to the available commands available .TP + A small command field for entering file names or options not provided in the standard interface (at the lower right). .TP + An area for status messages (at the lower left). .LP Inside the canvas, use the left and middle buttons to pick atoms, the right button brings up a menu for drawing and styling functions. Some commands (i.e., .I Hide and .I Complete) require the user to terminate a list of selected atoms with the middle mouse button. .LP .sp .SH CONTROL PANEL .LP The large control panel to the right of the canvas contains many items through which you may control .I MindTool. Some items are buttons which allow you to initiate commands, some are text fields which you type into, and others are choice items allowing you select a range. Use the left button to select items. Most items also have a menu which you may invoke with the right button for help. The frame header displays the file currently loaded and the default directory. .LP There is a text field at the lower right labeled either ``File:'', ``Cmd:'', ``Dir:'', or ``Label:''. A triangular caret points to the current type-in position. Typing in the text field enters the command. Note that no is needed for entering filenames, directory paths, or text labels. .LP Each item (Button) in the control panel is described below: .TP 12 .I Quit Exits the program immediately, without confirmation. .TP .I Save The current display will be saved, as is, to the file named in the command field, or if none is given, to the default filename shown in the header. All the commands needed to generate the display in its current state are saved along with the structure. .TP .I More Display the next structure in the file. Multiple structures within the same file are separated by four dashes (----). See INPUT FORMAT below. .TP .I Draw Redraw the current display. Useful when the screen gets corrupted. .TP .I cd Change the current working default directory to the directory named in the the command field. .TP .I Read Read the file named in the command field for display. If the file does not exist the user is prompted to correct the name. .TP .I Write Write the current display to the file named in the command field, or to the file name displayed in the header, if none is given. All the atoms that are visible in the current orientation are written. Note : if in zoom mode some atoms not visible will be written to the file. The zoom mode is only a local graphic construct. .TP .I Help display a help window. .TP .I Plot If no filename is specified, the current display, as shown, will be sent to the PostScript printer. If a filename is specified at the ``Cmd:'' prompt, an encapsulated PostScript file will be written. By default, the plot is in the Landscape orientation, however, mugs(1l) may be used on a saved PostScript file to scale, combine multiple files, or rotate to portrait orientation. .TP .I Zoom Zoom on a portion of the display by clicking the left mouse button and releasing, then adjust the rubber-banding box to frame the zoom portion and click again. .TP .I Pan Actually an ``unzoom'' button. This button will return the display to normal view. .TP .I Scale Will scale the display by the amount given at the ``Cmd:'' prompt. This is an absolute scaling, rather than a cumulative factor. If no scaling factor is given, the autoscaling feature will be toggled [off|on]. .TP .I Hide Click on an atom and hide it and its associated bonds from display. You may select any number of atoms to hide by clicking with the left mouse button and terminating your selection with the middle button. Note that the last atom to be hidden must be selected with the middle mouse button. .TP .I Hide None Display all atoms previously hidden. .TP .I Complete Complete the valence of an atom by displaying all the atoms that are bonded to it directly. Atoms are selected with the left button and the list is terminated with the middle button. This option is normally used after cutting a layer, a sphere or hiding atoms, when a complete molecule is wanted. i.e., cutting a sphere around a solute molecule followed by completing any solvent molecules. .TP .I Stereo Send a stereo plot to the PostScript printer. The .I viewing option is scaled for use with stereo glasses. The .I publication option will produce a plot at exactly double the size needed for viewing with stereo glasses. Note that directions should be given to the typesetter to scale the publication plots by 50%. .TP .I Grid Produce a background grid in the display useful for aligning text. The grid is evenly spaced in 0.25 inch intervals. .TP .I Add Full Clicking on two atoms will add a full bond between them. .TP .I Add Partial Adds a partial bond between the two atoms selected. .TP .I Delete Bond Deletes a bond of any type between the two atoms selected. .TP .I H-Bonds Draw hydrogen bonds between pairs of atoms. Both the acceptor and donor atoms must be heteroatoms. A hydrogen bond is considered formed if the H - - - A distance is less than the cutoff (default 2.5 A), and the D-H - - - A angle is greater than or equal to 120 degrees. Both the distance and angle criterion may be modified, see the notes on ADDITIONAL COMMANDS below. .TP .I Tell: These buttons will tell the .I Distance, .I Angle, .I Dihedral, and .I Number of atom(s) in the display. .TP .I Rotations: The .I X, .I Y, and .I Z, buttons are used to rotate the display around the indicated axes in a clockwise fashion (or counterclockwise for the negative buttons). .TP .I Slider bars: The slider bars display and set the angles of rotation about the respective axes. Click in the grey area to adjust. .TP .I Choice items: .TP .I Wireframe, Ball-n-Stick Set the display mode. In .I Wireframe mode, the bonds connecting the atoms are colored up to the middle point according to the atomic numbers. There are 3 .I Ball-n-Stick modes available, the default mode renders atoms as colored circles with opaque white bonds. The other modes are white balls and bonds, and white balls with colored bonds. See ADDITIONAL COMMANDS below. .TP .I Flat Bond, Round Bound Toggles between bonds represented by 4-point polygons and nicer looking cylindrical bonds. The .I Flat Bond mode is mainly used for very large data sets. .TP .I Orthographic, Perspective sets the mode of projection. .TP .I No Label, Symbol, Number .I No Label will turn off both types of labeling [default]. .I Symbol will mark atoms with alphanumeric labels, if these were provided in the file (up to 4 characters), or will use the atomic symbol if no labels were given. .I Number will label each atom with its sequential number, as determined from the input file. .TP .I Text: These buttons allow the user to .I Add, .I Move, and .I Delete text that is added to the display. To add text, enter a string at the Cmd: prompt and click on the .I Add button. Hold down the right mouse button in the drawing area to bring up a menu for changing fonts, text size, and text angle. The Angstrom symbol is given by the sequence ``\\A''. Superscripts are denoted by the ``^'' (caret) character immediately preceding the superscripted character (i.e., kcal mol ^-^1). Likewise, subscripts are given by the ``_'' (underscore) character. Note that the although the Angstrom symbol, superscripts , and subscripts will be plotted correctly on the PostScript device, they are not shown on the canvas. .TP .I Draw: These buttons .I Arc, .I Line, .I Arrow, and .I Delete allow the user to draw lines, arcs, and arrow heads on the display. These features are also available from the menu within the canvas, in addition to other styling features such as line widths and styles. The .I Arrow button adds an arrowhead to an existing line or arc. .SH ADDITIONAL COMMANDS .LP These commands may be entered in the text field. Two character abbreviations of all keywords are recognized and the input is free format. .TP .I set display normal This is the default. Will render the ball-and-stick display as colored circles with white (opaque) bonds. .TP .I set display reversed Will color the bonds magenta (a nice light color for the PostScript output) and the circles white. .TP .I set display clear Both bonds and circles will be white. Useful for illustrating atom numbering schemes. .TP .I set hbonds length [value] Will change the default maximum value (2.5 A) of length a hydrogen bond will be considered to exist. .TP .I set hbonds angle [value] Will change the default minimum angle (120 degrees) for hydrogen bond consideration. .TP .I cut top [value] will hide the atoms in the top layer of .I value angstroms thickness. .TP .I cut bottom [value] will hide the atoms in the bottom layer of .I value angstroms thickness. .TP .I cut sphere [radii] at1 {at2 ...} cuts sphere(s) of radius .I radii around atoms .I at1 at2 ... .TP .I cut sphere [radii] at1 to at2 cuts a sphere(s) of radius .I radii around ALL the atoms from .I at1 to .I at2, inclusive. For all the .I cut commands, one would normally finish by using the .I Complete command to fill in any dangling atoms/molecules. .SH INPUT FORMAT .LP The input is completely free format with the only requirement being that the first line of the input file contains two real numbers. By placing ``Mind'' as the first four bytes of the file, one can facilitate use of magic(5) numbers and the file(1) command. See the readme.filemgr file in the .I MindTool distribution directory. The ``#'' character placed in column one of any line will cause the remainder of the line to be treated as a comment. Lines starting with the ``$'' character can be used to include commands directly in the input file and will be executed before the molecule is displayed in the screen, i. e. ``$set model ball-n-stick'' .LP .I line #1: Mind RADFACT BONDFACT (2F) .LP .I RADFACT is the ratio of the displayed to the covalent radii ratio, a value of 0.3 gives a good ball-and-stick model. .I BONDFACT is the ratio of the bond thickness to the displayed atomic radius, a value of 0.666 seems to be adequate. .LP .I lines #2-end: ATOMIC_NUMBER X Y Z LABEL (I,3F,A4) .LP .I LABEL is optional. If present, only the first 4 characters are recognized. The default label is the atomic symbol. .I X, Y, Z are the Cartesian coordinates. Any additional character(s) in the line are ignored. Also, the ordering of the values is not important as long as the first integer number in the line is the atomic number, the first non-numeric string is the label, and the first three floating point numbers are the cartesian coordinates in the order X, Y, and Z. .SH EXAMPLE .nf Mind 0.275 0.666 # # s-cis Methyl Vinyl Ketone 3-21G//3-21G # 6 0.64889 0.30731 0.11489 C 8 0.64289 1.52160 0.11570 O 6 -0.59141 -0.48386 -0.10502 C 6 1.90717 -0.50133 0.33550 C 6 -1.74603 0.11679 -0.30768 C 1 -0.50123 -1.55227 -0.09077 H 1 2.74530 0.16333 0.48430 H 1 1.79088 -1.14047 1.20514 H 1 2.09565 -1.13781 -0.52337 H 1 -1.80204 1.18850 -0.31591 H 1 -2.65578 -0.42725 -0.46892 H $set model ball-n-stick .fi .LP The same file can contain more than one structure. The structures should be separated by a line that has at least four dashes (----) starting in column one. The following line should contain .I RADFACT and .I BONDFACT again (Mind 0.3 0.667). The .I More command reads the next structure in the file. .LP Up to 100 structures can be .I SuperImposed by separating the molecules with a ``%'' in column 1. Note that .I RADFACT and .I BONDFACT are not required after the ``%'' character. All the superimposed molecules will be shown in the screen simultaneously but no bonds will be made between them. .LP This program was written to provide a convenient interface to a rather useful molecular display program. Suggestions of features and enhancements are appreciated and will be taken under consideration when time permits. Any bugs should be noted and reported. .LP .SH SEE ALSO sunview(1), mugs(1L) .SH FILES .LP /usr/local/bin/mindtool .LP /usr/local/bin/mind .br /usr/local/bin/mugs .br /usr/local/icons/mindtool.icon .SH AUTHORS Julian Tirado-Rives .br James Blake .br Yale University .br Chemistry Department .br jim@doctor.chem.yale.edu .br julian@doctor.chem.yale.edu