1 DRAW On graphic terminals (that are supported, see TERMINAL) the default style is STICK (see DISPLAY). On NON-GRAPHIC terminals, no picture will be drawn; however you can still create output files which print the desired picture on appropriate printers. On all displays, the orientation of the axis is: positive X to the right, positive Y is up, and positive Z is out of the screen toward you. 2 BELL Causes the terminal bell to ring when the program is ready for a new top level command. If B ( not BELL) is entered, the bell will ring only the one time. 2 COMMAND This allows you to store one line of commands which will be executed evertime the NEXT command is executed. The intended use is to provide information about a specific portion of the data file. Therefore the INFORMATION command has been designed to allow more than one sub-command per line - but few of the other commands are so designed (yet.) As an example, if you store the string: "I N V Q", each time you type NEXT to read the next sequential part of the input file, DRAW will automatically display the two closest atoms (from the NEAREST (N) sub-command of INFORMATION), a listing of any atoms which exceed their "normal" VALENCE (V) and then the information command will QUIT (Q). DRAW will wait with the "DRAW>" prompt displayed. 2 DISPLAY Enters the DISPLAY mode. In this mode, you can select or modify parameters associated with the picture displayed or printed. 3 BONDS Selects and modifies the criterion by which bonds are selected to be drawn. 4 RADIUS The default bond selection criterion is RADIUS times 1.4 . If two atoms are within 1.4 times the sum of their covalent radii, they are connected by a bond. The multiplier is also selectable. 4 MATRIX This method is selected automatically if the input file contains bond order information. It is turned off if files are MERGED or EDITED in any way. 4 USER SELECTION This allows you to select two atoms to be bonded or to remove an existing bond between any atoms. The changes are made to the current bonds which are active. You make a new bond between atoms by entering the atom numbers: 5 6 will connect atom 5 and atom 6 with a bond. You remove bonds by making either of the atom numbers negative: -5 6 or 5 -6 will remove the bond between atoms 5 and 6. To remove all bonds to a specific atom: -7 * will remove all bonds to atom 7. 3 COORDINATES Changes the number of lines of cartesian coordinates shown on the screen. If you select 0, neither the file name nor column headings are printed. If any coordinates are displayed, DRAW will next ask which atom number should be at the top of the table. This allows display of the coordinates of any section of the geometry. 3 DUMMY ATOMS When you start DRAW, dummy atoms (symbol = XX) are not displayed on the screen. To allow them, enter the display subcommand +XX. 3 LABELS Select or remove type of labels used in picture. The default is NUMBER where the label is the number of the atom in the molecule. other choices are SYMBOL uses atomic symbols and MASK prevents drawing of labels. BOTH uses atomic symbols and atom numbers for labelling MASK prevents drawing any labels for carbon and hydrogen. USER allow you to enter the label to be used for each atom. 3 MAP (COLOR) Draw maintains a map of colors which it can use to differentiate different atoms on color capable terminals. In response to the MAP command, DRAW will display the current colors for the atoms in the displayed molecule. DRAW will ask if you wish to remove color differentiation. If you answer NO you will be asked to change the color map. 3 NAMODI Selects the NAMODI style of perspective drawing where atoms are drawn as circles with radii based on covalent radii and distance from the xy plane. Bonds are drawn with taper indicating perspective. The rate of drawing is intermediate between stick and Ortep. 3 NUMBER Allows or masks the drawing of any specific atom. Eg. -9 prevents the display of atom number 9 of the molecule. The atom is not removed from the molecule; it is simply not drawn in the current picture. 3 ORTEP Selects the Oak Ridge Thermal Elipsoid Plotting style. Atoms are drawn as circles (no thermal uncertainty). Bonds are drawn as tapered rods. This is a slow method of drawing. 3 PLOTTER Selects the type of PLOTTING device. The recognized types are: EPSON (FX-80) HP (Any device which uses HPGL) LA50 (DEC dot matrix printer) MPI-99 TIGER (IDS PAPER TIGER) 3 QUIT Leave the DISPLAY modification logic. The picture is re-drawn and will reflect all changes. 3 REMOVING ATOMS You can remove any atom or atom type from the display. For example, -13 will prevent atom 13 from being drawn, and -Si will prevent all silicon atoms from being displayed. Neither command will remove any atoms from the geometry discription. Atoms are re-allowed with +13 or +Si. 3 SCALE You may alter the amount of display area used by the plotting routines. This command will show the current scale factors for hard copy (HC=) and for screen (SC=). The values are altered by specifying which one to change (eg. SC=3 will draw pictures on the CRT which are 1/3 of the original size.) Changes made in the scaling are retained until specifically altered (see PLOT command at the top level.) 3 STICK Select STICK style of drawing. Atoms are shown by label (if labelling is enabled) only and bonds are single lines. No perspective is shown. This is the default mode and is the fastest mode of drawing. I suggest using the STICK mode to find the desired perspective and then switching to another mode for the final drawing. 3 SYMBOL Allows or masks the display of certain elements. Eg. -H prevents the display of all hydrogen atoms. The atoms are not removed from the molecule; they are simply not drawn in the current picture. Similarly, +XX will cause all dummy atoms to be drawn. The default is -XX and +all other atoms. 3 VIBRATION Selects a normal mode for display. The input file must be an output file from a FORCE calculation. The normal modes are identified by an integer. If mode 0 (zero) is selected, DRAW stops displaying vibrational information. If the input file does not contain vibrational information, DRAW will warn you. If you ask for a NEGATIVE MODE the mode will be drawn with the PHASE REVERSED. I.e., -2 is mode 2 in the opposite direction from 2. DRAW will re-orient the molecule to the orientation used in the force calculation EACH TIME a NEW MODE is chosen. When displaying vibrational modes many DRAW commands are not available. NOTE: Vibration is availble ONLY for STICK drawings at this time. 3 ZOOM If your terminal does not have a built-in ZOOM function, this may help you. Since DRAW automatically enlarges the picture to fill the allowed area of the screen, selecting only certain atoms to draw will cause a zoom effect. ZOOM works by preventing all atoms except those selected from being drawn. Once a mode is selected, you may show a higher part with '+' or a lower part withy '-'. 4 MANUAL You select the atoms to include in the picture. This is faster than -## if you want only a few atoms from a BIG molecule. 4 OPTIMIZED This selects only the OPTIMIZABLE ATOMS to view. 4 SURFACE Calculates a horizontal slice of the molecule to display. This allows successive views to be created to 'build-up' the 3-dimensional structure of a large molecule. 2 EDIT Allows modification of the group of atoms. Atoms may be added, removed or moved. 3 CHANGE Any part of the internal geometry may be changed by typing the atom number followed by a command letter and the new value, e.g.: 4 B 1.3 - will set a new bond length of 1.3 Angstrom for atom 4 4 ANGLE Changes bond angle, command letter: A. 4 BOND Will change the bond length, command letter: B. 4 DIHEDRAL Changes dihedral angle, command letter: D. 4 IA Changes the optimization flag for the angle. 4 IB Changes the optimization flag for the bond lenght. 4 ID Changes the optimization flag for the dihedral. 4 REFERENCE You can also change the atom numbers to which the selected atom is referenced. The command letters are: NA, NB, or NC. 4 SYMBOL Use the command letter T ( for type of atom.) 4 TYPE Will change the type (symbol) of the specified atom. Command letter: T 4 X If the MODE of operation is set to CARTESIAN (see MODE command) you may change the X cooredinate of the atom. 4 Y If the MODE of operation is set to CARTESIAN (see MODE command) you may change the Y cooredinate of the atom. 4 Z If the MODE of operation is set to CARTESIAN (see MODE command) you may change the Z cooredinate of the atom. 3 DELETE In EDIT you may delete any atom EXCEPT one of the FIRST THREE in the description. If the atom is not required for the correct placement of any subsequent atom, it will be removed and the internal numbering altered to reflect the change. If the atom to be deleted IS used as a reference for a later atom, you will be told and the atom will NOT be deleted. You can use the CHANGE to alter the connectivity of the atoms. 3 INFORMATION Enters the information routine directly to allow evaluation of editing changes. 3 MERGE FILES You can read a second geometry description into draw which will be combined with the existing file. This second file may be any format which DRAW recognizes. You will be asked to supply the necessary distance, angles and dihedral angles to specify the new molecule's exact relation to the current molecule. After merging, you can use all facilities of DRAW on the result. 3 MODE Selects CARTESIAN or INTERNAL coordinates for entering, reporting, or modifying coordinates of atoms. This affects ALL functions of EDIT. 3 NUMBER Typing the number of an existing atom allows modification of the atom. The current values are listed and you are prompted for new values. You must indicate which variable receives the new value. Eg.: T C changes the TYPE of atom to Carbon B 1.45 changes the bond distance to 1.45 angstroms A 114.5 changes the angle to 114.5 degrees D 300 changes the dihedral angle to 300 degrees NA 3 changes reference NA to atom 3 Eg. 13 T S B 1.4 A 92.5 D 309 will change atom 13 to a SULFUR with a distance of 1.4 A and new angle and dihedral. 3 NEW ATOMS Typing + causes the program to prompt for the coordinates of a new atom. If the current MODE is INTERNAL draw will prompt for the IC (internal coordinates) of the new atom. If the MODE is CARTESIAN the prompt will be CC. 3 REMOVING ATOMS Typing - causes the highest numbered atom to be deleted from the geometry description. It is actually removed (as opposed to the action of options in DISPLAY.) If you type -##, draw will attempt to remove atom number ##. If the specified atom is explicitly referred to by any atom in the description, it will not be deleted and you will be told why. If it is not used as a reference, it will be removed and all other atoms will be renumbered. 2 GIP Command: GIP [] [offset] This command produces a SPECIAL GIP (Geometry Interchange Program) file. This file is intended to be edited outside the DRAW program by any system editor to alter the numbering, connectivity, or cartesian position of the atoms. The default extension for the GIP file name is "GIP". OFFSET is a constant which is added to ALL atom connectivities. This helps in rearranging positions of atoms. ** NOTE: No special command is required to input a DRAW/GIP file, the DRAW program will recognize the special first line. 3 CONTENTS The file contains FOUR text lines followed by N+1 special cartesian geometry cards. The first text line is for internal identification by the DRAW program and should NOT be altered. The remaining three text lines contain the KEYWORDS, COMMENTS, and TITLE line from the original input file and will be reporoduced in any subsequent output file from the DRAW program. The remaining cards contain the ATOMIC SYMBOL, X, Y, and Z CARTESIAN COORDINATES and the "INTERNAL COORDINATE CONNECTIVITY" of the input file. 3 FILENAME If is given, the file will be named .GIP and can be edited via any system editor. If an extension is supplied, it will be used instead of ".GIP". If is not specified, the original input file name will be used with the extension ".GIP". 3 OFFSET If the optional offset is specified, all internal coordinate connection specifications will be offset by that amount. This is useful when two or more GIP files are to be concantenated to produce a larger molecular description. 2 INFORMATION This section provides information about the molecular geometry. 3 ATOM NUMBER The basic mode of this routine is geometry. The routine can provide: ## - atomic symbol, cartesian coordinates and bonded neighbors ##,## - distance between the specified atoms ##,##,## - angle descibed by the three atoms ##,##,##,## - dihedral described by the four atoms Eg. 5,21,3 will report the angle described by the three atoms. 3 COUNT Prints the number and types of atoms (including dummy atoms), the number of orbitals and number of electrons and the chemical formula. 3 FILES Lists the names of files used for input and various outputs. 3 INFORMATION Prints the first three lines of the input file (if internal geometry or archive) and, if the input file is an archive, will list various calculated values: Heat of formation, IP, dipole, reaction coordinate, reaction coordinate gradient, and gradient norm. 3 NEAREST Prints the numbers and separation of the two closest atoms in the molecule. 3 RADIUS RADIUS atom_number [ radius [ atomic symbol to exclude] ] Finds and prints all atoms which lie within a sphere centered on the specified atom. If desired, you can exclude all atoms of specified type. 3 VALENCE Prints all atoms which have more than the normal number of bonded neighbors. The selection of bonded atoms is described in the BOND subcommand under the DISPLAY command. 2 INPUT_FORMAT The DRAW program accepts molecular geometries described in internal coordinates. The default file type is ".ARC". The filename extension is NOT used to determine the type of data file. 3 ARCHIVE From an ARC file, DRAW will extract the heat of formation, I.P., dipole, and geometry with charges. If the archive file was created by a reaction coordinate path calculation, only the first point will be read-in. The NEXT command will read subsequent portions. 3 MOPAC_OUTPUT From an OUTPUT file, DRAW will extract the heat of formation, I.P., dipole, geometry, charges, bond order matrix, and normal modes of vibration. If the archive file was created by a reaction coordinate path calculation, only the first point will be read-in. The NEXT command will read subsequent portions. 3 BROOKHAVEN If the input file is from crystallographic sources, DRAW assumes it is in the BROOKHAVEN PROTEIN DATA BANK format. DRAW will ask which residues are to be selected. Residues are identified by number. Ranges of residues are selected by ##-##. DRAW will add the connectivity for the atoms. You may have DRAW input the individual ATOMS of each residue or input location for the entire RESIDUE. 4 ATOMS This function will read in all available atoms for each residue you request. The resulting structure will contain individual atoms without any identification of the residue each atom belongs to. 4 RESIDUE This function will read in special symbols consisting of the normal abbreviations of the amino acids. For each residue selected, the symbol will be placed at space coordinates corresponding to the center of the residue. In all other DRAW functions, these symbols will behave similar to individual atoms. 3 GIP This type of file is created by DRAW. DRAW recognizes it by the unique first line of the file. Do not change the first line. 3 DATA From a MOPAC data file, DRAW can only extract the keywords, comment lines, and geometry. 3 TEK DENSITY can create a special graphic file. This file contains primitive graphic commands which DRAW will read and translate to the selected terminal style. 2 LAST Undoes the last rotation. This command will not extend backward beyond an editor session. 2 MOVE Allows movement of any or all atoms in cartesian or internal space. You will be asked whether you wish to specify movement in CARTESIAN or INTERNAL coordinates. WARNING: Movement by INTERNAL coordinates is tricky and should normally be avoided. 2 NEW Forces DRAW to stop using the current file and prompt for a new file. You can tell DRAW to use the last file again by entering * for the file name. 2 NEXT The program will attempt to read another geometry description from the current input file. If the end-of-file is encountered, you will be prompted for a new file name. The format is Next [ R ] [ + [ n ] ] R will cause the next entry in the same input file to be read and drawn with the same rotations as are currently in effect. +n causes DRAW to skip over the next n-1 geometry descriptions in the current input file. If there are not n descriptions left, DRAW will process the end-of-file as described above. n causes DRAW to search foreward IN AN IRC file to find coordinate point n. If you are already past point n, DRAW processes end-of-file as described above. 2 OUTPUT Command: Output [[.DAT]] or * The program will write a file suitable for input to MOPAC. The first three lines of the file will come from the original input file. The internal coordinate description will reflect all changes made thru MOVE or EDIT commands.Specifing a file name will override the default name. Specifying * for the file name will use the default file name but ignore any directory of subdirectory prefixes. 2 PLOT Command: Plot [scale integer] [[.PLT]] or * The program will write a file which can be printed on the type of plotter selected via the PLOT subcommand of DISPLAY. The file will produce a picture which reflects the current display options in effect. The file IS NOT immediately dispatched to the printer. SCALE INTEGER is the per cent of full page to be to be used by the picture (default is 100%). Specifing a file name will override the default name. Specifying * for the file name will use the default file name but ignore any directory or subdirectory prefixes. 2 QUIT Exits the program and restores the terminal (if necessary) to non-graphic operation. If you have made any changes to the geometry via rotations of groups of atoms, or movement of groups of atoms, or by editing the description, the program will not allow you to exit without giving you a chance to save the modified geometry with the OUTPUT command. 2 REFLECT Format: REFLECT [PLANE] Performs a reflection about the specified plane (XY, YZ, XZ). This occurs about the absolute coordinate plane, not relative to the molecule. 2 RESET Causes all rotation information to be cleared and the molecule to be re-drawn from the internal coordinates. 2 ROTATE Allows rotation of any or all of a molecule. Rotations follow the RIGHT-HAND-RULE. Negative angles are allowed. For Cartesian and Euler rotations you may specify rotation about the origin by entering 0 (zero) for the atom number. 3 CARTESIAN Performs the specified rotation by the three CARTESIAN angles about the specified atom. Input: ATOM NUMBER, X (degrees), Y (deg), Z (deg) 3 EULERIAN Performs the specified rotation by the three Euler's angles about the specified atom. Input: ATOM NUMBER, THETA (degrees), PHI (deg), PSI (deg) 3 PAIR Performs the specified rotation about ANY TWO atoms in the molecule. Input: ATOM NUMBER, ATOM NUMBER, ROTATION (degrees) 3 GROUP You may specify any atoms in the molecule to be rotated. No information is requested until the type of rotation is started, then the program will ask for: NUMBER OF ATOMS IN GROUP, ATOM NUMBER [,ATOM NUMBER ...] 3 NOGROUP This will clear the GROUP request indicating that the whole molecule is to be rotated. 2 STRUCTURES DRAW comes with a set of skeleton structures. The structures include: PHENYL - phenyl ring with the H on C1 deleted C6CHAIR - chair cyclohexane with both H's on C1 deleted C6BOAT - boat cyclohexane with both H's on C1 deleted And various amino acids, see the manual for a current listing. 2 SYMMETRY The principal moments of inertia are calculated and the molecule is re-drawn oriented as follows: Center-of-mass at the origin, Principal axis in z direction (out of screen), Second axis in z direction (towards the right) 2 TERMINAL The type of terminal may be selected as: 3 NON-GRAPHIC Any terminal which is incapable of displaying graphics. 3 4010 This is compatible with any terminal which supports Tektronix 4010 commands as an alternate emulation. 3 4025 Specifically a TEKTRONIX 4025. 3 4105 This describes many of the TEKTRONIX 41XX series of terminals. The program will attempt to identify the actual model number from the terminal and adjust the commands to suit. 3 GIGI Provides limited support for DEC GIGI terminals. This mode uses REGIS graphics and may be compatible with other terminals. 3 RETRO-GRAPHICS This is designed for a RETRO-GRAPHICS modified VT102 terminal. 3 TERAK TERAK 8600 color terminal as supported at USAFA. 3 VT240 For a Digital Equipment Corporation (DEC) VT240 or related terminal. 3 APCOL For an Apollo Color Workstation. 3 APMON For an Apollo Monochrome Workstation. 3 BIG-COLOR For a full screen display on Apollo Color Workstations. 3 BIG-MONO For a full screen display on Apollo Monochrome Workstations. 3 XWIN For any standard X-Window terminal or workstation. X11 R3 2 VERSIONS Below is a summary of changes between versions. 3 1.00 This is the first version contributed to QCPE. You should NOT HAVE an earlier version. If you do, contsct QCPE for a more recent one. 3 2.00 New terminals supported: RETRO-GRAPHICS ON VT102 DEC VT240 Bit map graphics printer selection via PLOT subcommand of DISPLAY. Printers which I support are: IDS PAPER TIGER EPSON FX-80 DEC LA50 New input file supported: IRC output from MOPAC. New display mode: normal modes of VIBRATION via DISPLAY Enhanced labelling: LABEL subcommand of DISPLAY allows more flexibility in choosing labels for atoms NEXT command: now allows another option [+]n. BUGS FIXED: One of those rare things: bugs was located and exterminated in the EDITor command. It caused DRAW to loose track of atoms in the display when you deleted more than one atom without re-drawing the picture. IT IS GONE!!!