Copyright: Grigoriy Zhurko


ChemCraft basic information

Browsing output files:

An output file can be opened via "File/Open" menu item. When a file has been read, it is divided into separate elements presented in Data Explorer (the hierarchical list at the left): individual geometries, vibrational modes and other. By clicking on the nodes of the list one can view individual geometries, vibrations from the file. There are five view modes for these elements: Image (picture of the molecule), Abstract (some conspectus of the element), Source (the text of the output file), Coord (Cartesian coordinates of the atoms in the molecule), Image/Abs. (split mode with picture and abstract). Image mode is the primary. Buttons and checkboxes on the panel at the left, which appear when clicking on the items of the list, allow one to visualize charges on atoms and other atomic properties, occupations and energies of bonds (checkboxes "Show atomic properties", "Show bond properties"), dipole moment (checkbox "Show dipole moment"), graphs with IR or Raman spectra or potential energy surface (buttons "View spectrum", "View scan graph"), show the directions of vibrational modes or forces on the nuclei (checkboxes "Show displacement vectors" for vibrations, "Show forces" for individual geometries), etc.

If the output file contains bonds between atoms, calculated from population analysis (Mulliken or NBO), ChemCraft renders these bonds on the image of molecule; otherwise, the bonds are identified automatically using the distance algorithm. If the checkbox "Show bond properties" is enabled for an individual element of the list, this is evidence that the bonds have been read from the file for this geometry. For Gaussian computations, POP(NBO) must be specified in the input file for bonds to be printed in the output file. In GAMESS-US files the bonds are usually printed; by default, only bonds with bond order not less than 0.25 are shown on the image (this value can be altered in "Tools/Preferences/Gamess").

Interface basics:

When working with the image of molecule (Image mode), these operations can be used:

Left-click	Select/deselect atom.

Right-click	Deselect all atoms.

Right-click+dragging	Rotate molecule.

Ctrl+right-click+dragging	Translate molecule in X-Y direction.

Shift+Ctrl+right-click+dragging	Translate molecule in Z direction.

Double left-click	Change the type of atom/bond, caption on it.

Double right-click	Change the atom/bond style (size, color, etc).

       The molecule can be also rotated/translated using buttons on the toolbar to the right of the  main window and keys Num1-Num9. One can alter the point which the molecule rotates around pressing button [image] (see Interface notes).

Working with molecular structure

To examine the value of a geometrical parameter (distance, angle, dihedral), one should select 2, 3 or 4 respective atoms by left-clicking: the value will be presented in textbox at the bottom. For selection of new atoms, old atoms must be first deselected by right-click. The button "Show" (to the right of the textbox) displays the value of current parameter on the molecule's image. The chosen geometrical parameter can be altered by entering a new value in the textbox and pressing the "Set" button. If the button [image] is pressed, the coordinate of only last selected atom would change; if the button [image] is pressed, first and last selected atoms would move symmetrically. Other atoms bonded to the selected ones will move along with them; if that is undesirable, one should manually delete bonds or add new bonds by selecting pairs of atoms and pressing Ctrl+B. For additional details on such geometry modifications see see Constructing molecules.

The Coord mode allows one to import or export coordinates of atoms in text format (in angstroms or Bohrs). On switching to this mode the text with coordinates is refreshed according to current molecule; on switching from this mode to another the molecule is refreshed by the text (if there have been changes made in the text). The format of entered text is very free (e.g. sections with atomic coordinates from Gaussian or GAMESS-US output files can be entered). The buttons Copy and Paste can be used to quickly copy the text into clipboard or into the textbox from the clipboard. Pressing Paste twice automatically switches to Image mode. The text is automatically refreshed by current molecule on pressing "Show sequence" or "Angstroms/Bohrs" so pressing these controls can restore accidentally corrupted or replaced text.

The "Edit/Drag atoms" menu item or button [image] allows the atoms on the molecule's image to be moved using the mouse. While dragging an atom one can move it in the Z direction (in parallel with the view) using the keys Num2/Num8.

ChemCraft provides an iterative algorithm for constructing molecular geometry according to an arbitrary set of geometrical parameters. The "Tools/Console editor" menu item opens a window, where one can enter required values of geometrical parameters in text format.

Menu items "Edit/Add atom" and "Edit/Add fragment" allow the construction of new molecules built from individual atoms or molecular fragments (radicals, etc). The possibility to edit the set of standard fragments and supplement it with custom fragments is provided ("Edit/Add selected fragment to database"). Keys Ctrl+C, Ctrl+V allow the transfer of fragments via clipboard (e.g. to copy a radical from one molecule to another). See Working with molecular fragments for more details.

Using molecule rendering possibilities:

The image displayed can be saved as a file ("File/Save image" menu item) or copied into the clipboard ("Edit/Copy page" menu item or button [image]).

The menu "Display" allows one to choose the graphical scheme, in which the molecule is rendered. Each scheme is defined by a set of parameters, such as sizes and colors of individual atoms and bonds, parameters of lighting, etc. The "Display/Customize" menu item allows the parameters in current schemes to be altered.

Different labels of various styles can be shown on atoms and bonds by double-clicking on them, as well as by using "View/Labels on atoms" menu items or buttons [image], [image] and further. ChemCraft also allows labels and lines to be added to the picture of molecule from the "Auxiliary designations" panel, enabled by the button [image] (at the bottom). For more detailed description see Obtaining publication-ready pictures.

Visualization of molecular orbitals:

ChemCraft extracts tables of molecular orbital coefficients from the output files, which can be visualized in the form of isosurfaces and colored figures. The program can read orbitals from GAMESS/Gaussian output files and Gaussian Checkpoint files (.chk, .fch), as well as computed maps in Gaussian Cube files and ADF ASCII TAPE41 files. For Gaussian computations, "#P GFINPUT POP(FULL)" should be specified in input file for orbitals and basis set information to be printed in output file.

To visualize an orbital, one should open an output file and select the "Tools/Orbitals/Render molecular orbitals" menu item, or select an item in the list at the left (e.g. "Optimized geometry") and press the "Tools" button (below the list), then "Render molecular orbitals". In window that appears one should select the required orbitals and press "Ok". Then in the list to the left choose the desired orbitals and press "Show isosurface" (an isosurface of value specified in "Value" textbox will appear) or "Show mapped plane" (a colored plane will appear with colors from blue to red corresponding to values in "Values range" textbox). The button "Plane position" allows the position and orientation of rendered plane to be altered. For antisymmetric orbitals, the "Both-signed" button should be pressed. The "Keep this surface" and "Delete all" buttons can be used to obtain multiple isosurfaces on the picture. For more details see Working with cubes.

Special utilities:

The  "Tools/Build Z-matrix/" menu item allows one to obtain a Z-matrix in text format by clicking atoms in current structure and specifying some additional information (e.g. whether current parameter is an angle or a dihedral). Before using this utility one should preliminarily obtain the structure of the molecule in Cartesian coordinates. For more details see see here.

The "Tools/Create input file/GAMESS-US…" menu item allows a section of GAMESS-US input file with non-standard basis sets to be obtained quickly. The sections $DATA, $ECP are created from descriptions of basis sets in text format, which can be obtained at PNNL's Basis Set Order Form webpage (http://www.emsl.pnl.gov/forms/basisform.html).

ChemCraft provides the possibility to save in GAMESS/Gaussian input format molecular orbitals read from a file, which may be used as an initial guess for a new calculation ("Tools/Orbitals/Convert orbitals into input format/" menu items).

ChemCraft can convert fractional coordinates, used in crystallographic measurements, into Cartesian. For details see here.

When working with NMR computations (GIAO, CSGT) a simple utility for obtaining tables of chemical shifts, averaged within specified groups of atoms can be used (see here).

The menu items "Edit/Set point group" allows a specified point group to be easily applied to the molecule, if its geometry is satisfactory close to required group.

Additional remarks:

If the molecule is too big and slowly rendered, choose "Display/Quick".

If ChemCraft doesn't identify the bonds in molecule correctly, one can manually set all bonds via Ctrl+B (no bond should be missed) and choose "Tools/Supporting/Update possible bond lengths table": the tables of standard bond lengths will be automatically adjusted and next time the bonds must be identified as they were set.

ChemCraft can correctly visualize incomplete calculations (e.g. unfinished optimization, scan jobs). The output files being computed can also be opened.

Most of the program's functional possibilities can be accessed through menu items of the main window. They are supported by individual help pages, evoked via F1. Most widely-used items are duplicated by buttons under the menu. This help page can also be activated from main window by pressing F1.


Interface notes

The displayed molecule is rotated or translated using the mouse or the buttons on the right-hand panel. One can rotate the molecule by scrolling the mouse with the right mouse button pressed and translate the molecule in the X and Y directions by pressing the right button + Ctrl. The right button + Ctrl + Shift moves the molecule in the Z direction. The point which the molecule rotates around can be specified: menu item "View/Update rotation center" or button [image] places the rotation point at the coordinate center of selected atoms, or if no atom is selected, at the center of whole molecule.

Double-clicking on an atom or a bond shows a dialog box from which both the type and the label may be edited. Double-right clicking on an atom or a bond allows visual properties (color, size, etc.) to be edited.

Pressing Ctrl+Numbers 5...0 remembers the current "camera" position (restored by 5...0).


Constructing molecules

ChemCraft provides different possibilities to build molecules and change their geometry, which are useful for preparing an initial approximation for computations, and other purposes. In many cases, a molecule can be easily built using standard molecular fragments (see Working with molecular fragments).

If two atoms are selected, pressing Ctrl+B inserts or removes a bond between them.

One can modify any geometrical parameter (bond length, bond angle, dihedral) using the textbox at the bottom of the main window. When one selects 2, 3 or 4 atoms, the value of corresponding parameter is shown in the textbox. Attention must be paid to the sequence in which the atoms are selected. If one modifies the value and presses the "set" button, the positions of atoms are adjusted to the new value. Either the coordinates of last selected atom will change, if the button [image] is pressed, or the coordinates of first and last selected atom will change symmetrically with the button [image] pressed. Other atoms bonded to the selected ones will move along with them, so it is often important to insert or remove bonds, before changing a geometrical parameter, via Ctrl+B. Specifically, the coordinates of all atomic groups bonded to last (first) selected atom (i.e. directly bonded, not through intermediate second/third selected atoms when changing angle/dihedral) but not directly bonded to opposite first (last) selected atom, will be changed (the coordinates of these atoms would be translated in parallel with last (first) selected atoms, when a distance is changed, or rotated along second/third selected atom together with last (first) selected atom, when an angle/dihedral is changed).

If two or more atoms are selected, pressing Ctrl+A and choosing "X" places a dummy atom into the coordinate center of selected atoms. This feature can be useful in complicated geometrical modifications.

The program allows the coordinates of atoms to be changed by "dragging" them using the mouse. The atoms or fragments are "dragged" in dragging mode toggled by the "Edit/Drag atoms" menu item or the button [image]. Dragging an atom with Ctrl pressed activates dragging of whole molecule (bonded group of atoms).

A group of atoms can be also rotated along the axis, defined by two selected atoms, via "Edit/Rotate along selected" menu item. This opens a window with a scrollbar, which when moving, the atoms bonded with second selected atom are rotated.

In some cases, it is helpful to perform complex geometry modifications using the Console Editor ("Tools/Console editor" menu item). It provides an iterative algorithm for applying new values for an arbitrary set of geometrical parameters. The values of parameters are entered in text mode (e.g. "r(1-2)=2.1, a(3-2-1)=120,…").

If an undesired change of coordinates is made, Ctrl+Z can be used.


Working with molecular fragments

ChemCraft allows standard groups of atoms (fragments) for use in building new molecules. To add a new fragment to a displayed structure, select the "Edit/Add fragment" menu item, then choose the required fragment from the list in the Fragments Editor window. If you choose fragment-radical with one selected atom in current structure, the new fragment will appear near this atom, connected to it with a bond. If the selected atom is a hydrogen or a dummy atom bonded with some other atom, the new fragment will be bonded with that bonded atom, replacing the selected hydrogen or dummy atom. If there are two or more selected atoms, the new fragment will be bonded to the atom which was selected first, replacing other selected atoms (this feature can be convenient for changing one radical to another). The similar actions are done when one adds individual atoms.

One can add any group of atoms in displayed structure to the set of fragments. To do this, select the atoms which form a fragment and choose "Edit/Add selected fragment to database", then chose a directory and press "Ok". If the fragment is a radical, the atom bonded with the  outer molecule must be selected first. To delete the fragment from the set, or change its directory, choose "Tools/Supporting/Edit fragments database".

Pressing Ctrl+C copies the fragment of selected atoms into the clipboard (in text format), pressing Ctrl+V adds the fragment from clipboard to current molecule. The rules of atoms selection are the same as for using "Add fragment" and "Add selected fragment to database" menu items.

Here is an example of building acetone molecule:

 - Clear the displayed structure (choose "File/Clear" menu item).

 - Choose "Edit/Add fragment", then select -CH3 (subitem in the "-R" directory).

 - Select the transparent dummy atom in fragment.

 - Choose "Edit/Add fragment", then select -CO- (subitem in the "-R-" directory).

 - Select the transparent dummy atom bonded to the added C atom.

 - Choose "Edit/Add fragment", then select -CH3.

 - The molecule is built, but the dihedral angles along the C-C bonds may correspond to wrong conformation. To change the conformation, select O,C,C,H atoms which form dihedral angles and change their values in the textbox at the bottom of the window, then press the Set button.


Working with cubes

     These buttons and textboxes allow to visualize and perform operations with cubes:

Show isosurface	Draws the isosurface of current cube;

Both-signed	If pressed, two isosurfaces will be rendered on the image, with positive and negative contour values;

Contour value	Defines the boundary value which outlines current isosurface;

Style	Allows the style of current isosurface to be changed.

Map other	If two or more cubes are present, this textbox allows the isosurface of current cube to be colored by the values of another cube;

Show mapped spheres 	Renders spheres around each atom colored by the value of current cube (the sizes of the spheres are proportional to van-der-Waals radii);

Scale	Scales the sizes of mapped spheres;

Show mapped plane	Renders a plane colored by the value of current cube;

Plane position	Allows the position and orientation of the mapped plane to be specified;

Values range	Defines the interval of values in which the points of isosurfaces, mapped spheres and mapped planes are colored (from blue to red);

Keep this surface	Saves the current isosurface so one can render another isosurface at the same time (the parameters of saved isosurface cannot be changed);

Clear all	Clears all saved isosurfaces;

Hide atoms	If pressed, all atoms and bonds become invisible;

Load atoms from file	This button is enabled if no atomic coordinates have been present in cube file. This button allows atoms to be read from a specified file for current cube;

Add cube	Opens another cube file and adds the data from it to current cubes list (it allows different cubes to be compared or cube operations to be performed);

Operations 	Allows different cube operations (addition, production, etc) to be performed with the available cubes. The result of an operation will appear as an additional cube in the list. At the moment ChemCraft can only perform operations with cubes equal in size and coordinates (multiple cubes which are equal can be obtained with Gaussian by explicitly specifying their size and origin, or if these are different molecular orbitals in one file).

      See also:

      Obtaining isosurfaces of properties other than molecular orbitals.


Obtaining publication-ready pictures

ChemCraft allows high-quality pictures of molecules to be obtained, which can be used for writing papers. The picture of the current molecule can be saved to file via the "File/Save image" menu item, or copied into the clipboard via "Edit/Copy page" or button [image]. Molecules can be rendered in different graphical styles. One can alter the color and style of each atom or bond, enable/disable lighting, drawing shadows and other effects changing the properties of current graphical scheme (see Display menu).

Use Ctrl+B to add or remove bonds in molecule. To alter the type of a bond (e.g. to make the bond dotted), double left-click on it.

The picture of the molecule is saved to a file or copied into the clipboard in better quality than rendered on the main window; pressing Ctrl+Q shows the picture to be saved.

The molecule's image can be decorated with static objects, such as labels and lines. To add such object to the picture, click on a button on the "Auxiliary designations" toolbar (enabled via the button  at the bottom of the main window), and then pass the mouse cursor on the image with left mouse button pressed. Property labels can also be added by selecting 2, 3 or 4 atoms and pressing the "Show" button at the bottom of the main window: corresponding structural parameter (interatomic distance, angle or dihedral angle) will be rendered on the image. If one saves the picture of current molecule as a metafile, all static objects will remain accessible for editing using other software (for example, in a Word document).

The position of labels and lines, the width and height of labels, length and orientation of lines, position and length of arcs can be changed by dragging them using the mouse. Left-clicking on a label allows the text to be changed and right-clicking on a label or a line allows the properties to be changed (e.g. font for label, pen style for line). The "View/Structural parameters/Style" menu item allows the style of all objects representing structural parameters, in particular number of digits after decimal point to be changed.

The last button on the "Auxiliary designations" toolbar allows various ActiveX objects to be added (for example, a small Paintbrush picture). In the current version of ChemCraft, working with such objects is of limited implementation.


Console editor

This window allows various geometrical parameters to be changed (bond lengths, bond angles, dihedral angles) in the displayed molecule. To set new parameters in the structure, type their values in the textbox in the following format:

r(n1-n2)=value

a(n1-n2-n3)=value

d(n1-n2-n3-n4)=value

Here  n1,n2… are the numbers of atoms in the molecule, value - digital expression for the parameter or the expression of another parameter (for example, r(1-2)=r(1-3)). It is useful to press [image] button before using this window. Several parameters of equal value can be entered in one line, for example: a(2-1-3)=a(2-1-4)=a(3-1-4)=120). Here are some examples of using this utility:

r(1-2)=r(1-3)=r(1-4)=r(2-3)=r(2-4)=r(3-4)=3

The atoms 1,2,3,4 will form an equilateral tetrahedron with the edge length of 3 angstroms.

a(2-1-3)=a(2-1-4)=a(3-1-4)=30

r(1-2)=r(1-3)=r(1-4)

r(2-3)=2

The atoms 1,2,3,4 will form an isosceles pyramid with the apical angles of 30 degrees and the base edge's length of 2 angstroms.

Note: In some cases, it is necessary to set the initial positions of atoms close to the required geometry before using this editor. In future versions the algorithm possibly will be improved and some other functions will be added.


Preferences window

The program's settings can be changed in this window.

                       Common preferences:

  -  Show hint at startup	If checked, the first help window will appear when the program starts.

  -  Auto redraw anti-aliased picture	If checked, a better quality picture of molecule will be automatically drawn when the molecule has not been scrolled for 3 seconds (in current version of the program, this feature is not implemented in the best way).

  -  Any extensions for GAMESS/Gaussian	If checked, Gaussian and Gamess output files can have any extensions; otherwise, they must have the ".out" extension to be loaded via "File/Open" with "Gaussian/GAMESS files" filter. This option is somewhat obsolete.

  -  View orientation	Selects the orientation of coordinate axes in startup view (by default it is the one used in GaussView and other visualization tools).

                       Interface preferences:

  -  Key scroll sensitivity 	Defines the speed of movement, rotation and scaling of a molecule on key scroll.

  -  Mouse scroll sensitivity	Defines the speed of movement, rotation and scaling of a molecule on mouse scroll.

  -  Atoms selection	Defines the style of selecting the atoms.

                       Gaussian preferences:

  - Formchk utility	Specifies the pathname of "formchk.exe" program for converting Gaussian Checkpoint files to Formatted Checkpoint (a dialog box for choosing the pathname is automatically shown when opening a Checkpoint file (*.chk) for the first time).

                       Gamess preferences:

- Bond order threshold for visualization	If a value is specified in this textbox, only bonds with order not less than this value will be shown on the image. This option can be useful if too many dotted bonds are rendered (the "Show bond properties" checkbox in the Data Explorer window shows all bonds regardless of this value).


GAMESS input creation window

Here input section for Gamess jobs are generated from the current molecule. The $DATA, $ECP sections are generated when you choose one of the pre-defined basis sets (in "Available basises" list). The checklist "Current basis set" allows separate basis sets for different atom types to be specified: when you choose new basis set in "Available basis sets" list, only checked atom types are affected. If "Multiselection" checkbox is checked, you can choose a combination of several basises (for example, to use diffuse/polarization basis sets).

The button "Customize basises" allows the collection of pre-defined basis sets to be edited (see Customizing pre-defined basis sets). The button "Add gaussian" allows custom gaussian functions to be added to the current basis set. It opens a dialog window where one can choose the type of gaussian function and values of exponents and contraction coefficients in the format "exponent/coefficient" (if only one digit is specified, contraction coefficient is assigned to 1.0).


Z-matrix builder

The menu item "Tools/Build Z-matrix/" allows a Z-matrix to be generated in text format. Before using this feature one must first have a structure of the molecule in Cartesian coordinates. In fact, this utility allows one to convert molecular structure from Cartesian to Z-matrix coordinates, not to build a new Z-matrix. For creating a new structure one can use different possibilities of ChemCraft (see Constructing molecules), or, for example, perform a calculation of geometry optimization on a "cheap" method in Cartesian coordinates.

Each line in the Z-matrix defines one new atom and contains information on its connectivity with previously defined atoms (a distance, angle and a dihedral, formed by this new atom and three specified atoms). When Z-matrix Builder is activated, the user is prompted to click on the atoms in sequence corresponding to desired Z-matrix and specify some additional information concerning parameters of the Z-matrix. The values of distances, angles and dihedrals are automatically calculated by the program using the coordinates of the atoms in the molecule.

Here is an example of using this feature. When the building of Z-matrix starts, one must click on atom N1 to be placed at the first line of the Z-matrix. Then one clicks on atom N2 forming the second line; any atom in the molecule except the atom N1 can be clicked. After that, the atom connected with atom N2 is clicked; for the second line that can be only the atom N1. Then one should specify the type of parameter R(N1-N2) at the right window: whether this distance is an independent parameter (in "variables" section) or a fixed distance specified in the body of Z-matrix (distances are usually chosen as independent parameters). After the type of parameter is chosen in the list and the button "Ok" is pressed, the atom N3 is clicked, which will form the third line of Z-matrix, and  atoms N1 and N2 in any sequence, with which the atom N3 will form a distance and an angle. The distance can be chosen as a fixed parameter, a new independent parameter, or equal to previously chosen parameter R(N1-N2), if the types of atoms are the same. The angle can be chosen as a fixed parameter or an independent parameter. For the fourth and subsequent lines, the same actions should be performed specifying three parameters (distance, angle, dihedral); additional menu at the top of the window allows one to choose whether the last parameter is a dihedral or a second angle. The type of current choice is indicated by the text line at the top of the main window. The button "Finish" finalizes the Z-matrix construction and shows it in separate window; the button "Show" displays this Z-matrix without finishing its creation. The buttons [image] and [image] allow to undo/redo the last choice of atoms and parameters (nevertheless, in case of errors, if the Z-matrix is not clearly designed, it must be often rebuilt from the beginning).

In some cases before activating this tool one should add dummy atoms to the current molecule: Ctrl+A, then "X". If one selects two or more atoms and adds a dummy atom to the molecule, this atom is placed into coordinate center of selected atoms.


Atomic properties table

This form can be useful for quick obtaining tables of atomic properties. It was designed mostly for working with NMR computations (GIAO, CSGT). The NMR isotropic shielding values can be read from output files and shown via "Show atomic properties table/..." menu item activated by the "Tools" button in Data Explorer window (under the hierarchical list at the left)

At the "groups of atoms" list one types the numbers of the atoms in current molecule. Each line can contain one or several atomic numbers divided by any separators (spaces, commas). When the "Update table" button is pressed, the atomic properties corresponding to entered numbers are shown at the right list, averaged within specified groups of atoms. The "Recalculate values as" checkbox allows recalculation of atomic properties (e.g. to convert isotropic shieldings into chemical shifts).


Printing molecular orbitals in input format

This form allows molecular orbitals read from a file to be saved as an initial guess for new calculation. For example, with this utility one can use Gaussian computed MOs as an initial guess for GAMESS(US) job. If the orbitals contain internal functions (5d, 7f), they can be converted into either Cartesian functions (6d, 10f) or printed as internal (when writing orbitals in GAMESS(US) input format, such orbitals can only be converted to Cartesian). ChemCraft takes into account the fact that the sequence of F and G functions is not the same in different quantum chemistry packages.

The checkboxes "Print atomic coordinates", "Print the basis set as non-standard" enable printing of molecular geometry and basis set parameters together with eigenvectors. If these options are disabled, one must be sure that the molecular geometry, including axes orientation, and the basis set are the same in the file from which the orbitals have been read and the input file where the eigenvectors should be written to. Note that this utility does not support printing of ECPs, so they must be specified in the input file manually if used in the computation.

Notes for GAMESS(US) users:

When eigenvectors are printed in the GAMESS input file as cards, usually only C1 point group should be specified (otherwise the orbitals can be read improperly because of principal axes change in the molecule).

Notes for Gaussian users:

With Gaussian98 usually NOSYMM must be specified in the route section of input file. Otherwise the orbitals are re-oriented by Gaussian and can be read improperly. With Gaussian03 these problems usually do not occur, but in some cases NOSYMM must still be specified in input.


Choose orbitals window

In this form one chooses the orbitals, for which a cube (3-dimensional grid of orbital density values) should be built. If the checkbox "Save to cube file" is checked, these cubes are saved to a file after building. The textbox "Map points per angstrom" determines the density of the grid (total number of points is proportional to this value in third power). The textbox "Map size expansion" determines how long the cube would be extent over the molecule (i.e. the size of cube). The total number of points is shown at the left bottom corner; the time of building each orbital is proportional to this value. The button "Explicit coordinates" allows the exact number of grid points and its coordinates to be specified.


Customizing pre-defined basis sets window

Each basis set is defined by a separate text in Gamess format, which can be obtained from PNNL's Basis Set Order webpage (http://www.emsl.pnl.gov/forms/basisform.html). The text consists of sections like "GALLIUM      ! (4s,4p)->[2s,2p]…" (describing basis functions), "TE-ECP GEN 46    4…" (describing ECP). The sections in the text can be given in any sequence. Comment lines are not read by the program. All defined basis sets are stored in "basises.txt" file in ChemCraft root folder.

To obtain basises for all available atoms, one should type lines like these at PNNL's webpage:

H,He,Li,Be,B,C,N,O,F,Ne,Na,Mg,Al,Si,P,S,Cl,Ar,K,Ca,Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Ga,Ge,As,Se,Br,Kr,Rb,Sr,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd,In,Sn,Sb,Te,I,Xe,Cs,Ba,La,Ce,Pr,Nd

Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu,Hf,Ta,W,Re,Os,Ir,Pt,Au,Hg,Tl,Pb,Bi,Po,At,Rn,Fr,Ra,Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr,Ku,Ns.


Conversion between fractional and Cartesian coordinates

The "Tools/Crystallography tools/" menu item allows fractional coordinates used in crystallographic measurements to be converted into Cartesian coordinates, and conversely, using data on unit cell: a, b, c, α, β, γ. To convert fractional coordinates to Cartesian, firstly open a .xyz file with fractional coordinates of the molecule, or import the coordinates from the clipboard using Coord mode. The molecule will appear distorted. Then select "Tools/Crystallography tools/recount fractional to Cartesian" and type the cell parameters. Conversion of Cartesian coordinates into fractional is done in the same way.

The formulas for conversion were taken from the following paper: J. L. Sussman, S. R. Holbrook, G. M. Church, S. Kim. Acta Cryst., 1977, A 33, 800-804.


File menu

Clear	Clears the displayed structure and removes all additional objects on the screen (lines, labels);

Open	Allows a file with results of a calculation or a molecular structure to be opened. When opening a calculation file, all data read from it is represented in the Data Explorer window, which is shown automatically (at the left);

Save structure	Saves displayed molecule as ".xyz" file;

Save image	Allows the picture of displayed molecule to be saved;

Exit	Closes the program.


Edit menu

Undo	Restores the molecular structure changed by last modification;

Redo	Returns the structure after Undo action;

Add atom	Adds a new atom to the displayed structure. If there is one selected atom, the new atom appears near it, connected to it with a single bond;

Add fragment	Adds a molecular fragment (ligand or radical) from the set of standard fragments to current structure. As for atoms, fragments-radicals will appear connected to the atom which is selected (see Working with molecular fragments);

Delete	Removes all selected atoms or selected objects (lines, labels);

Copy	Remembers the fragment of selected atoms by copying into the clipboard (in text format). If the selected fragment is a radical, the atom by which it is bonded to outer molecule must be selected first;

Paste	Adds the fragment from the clipboard to displayed structure;

Add selected fragment to database	Adds the fragment of selected atoms to standard set of fragments. To delete the fragment from the set, or change its directory, choose "Tools/Supporting/Edit fragments database". The fragments database is stored in "fragments.bin" file;

Add/remove bond 	Inserts a single bond between two selected atoms, or removes the existing bond;

Unite two groups	Before clicking this menu item, two dummy or hydrogen atoms belonging to different bonded groups must be selected. These fragments will be united into one molecule;

Translate/rotate atomic coord.	Opens a window which allows one to perform geometric transformations of atomic coordinates in current molecule (translation, rotation);

Make small random displacement	Adds a random shift to x, y, z coordinates of all atoms in molecule (we used this possibility to determine whether the structure is a local minimum or a saddle point, when the second derivatives are too expensive to be used);

Rebond 	Identifies bonds in displayed molecule, using the distance algorithm;

Superpose fragments	Places second selected fragment into coordinates center of first selected fragment (the fragment is identified by the bonds);

Clean	These subitems allow the positions of atoms in the whole molecule or selected fragment to be adjusted to more closely match chemical intuition:

  Set standard bond lengths	Positions the atoms to set standard values for bond lengths. The new values are shown on the molecule's image; to hide them, right-click on the screen;

  Set standard bond angles	Positions the atoms to set standard bond angles;

  Set all	Positions the atoms to set standard bond lengths and bond angles, simultaneously;

In current version of the program, standard bond lengths are estimated only for elements from H to I. The algorithm of estimation does not take into account the p-coupling between bonds and can miss in some cases. Also, cleaning does not work with rings.

Set point group	These subitems allow a symmetry point group to be applied to current molecule. The program automatically finds appropriate group axes orientations and allows the user to select an orientation;

Set Z-matrix orientation	Changes the coordinate system to place the atoms in Z-matrix orientation (first atom becomes the coordinate center, second atom lies on Z axis, third in XZ plane);

Set principal axes	Changes the coordinate system so X, Y, Z axes become the principal axes of current molecule. The procedure also shows principal moments of inertia in textbox at the bottom. The algorithm of axes determination (based on diagonalization of the inertia tensor) was taken from the source code of GAMESS program.

Drag atoms	Toggles on/off the dragging mode, which allows the displayed structure to be edited by "dragging" atoms in it;

Rotate along selected	Allows the rotation of a fragment along the line connecting two selected atoms;

Copy page	Copies the picture of the displayed molecule into the clipboard.


View menu

Isometry	Switches to isometry mode;

Perspective	Switches to perspective mode;

Update rotation center	Changes the point which the molecule rotates around on scrolling (see Interface notes);

Better view	Moves the "camera" to view the molecule better foreshortened;

Center	Moves the "camera" to view the molecule at the center of the image, filling 4/5 of its width or height;

Draw export picture	Renders anti-aliased picture of molecule on the image;

Show axes	Displays X, Y, Z axes on the molecule;

Labels on atoms	These subitems allow different labels on atoms in displayed molecule to be shown:

Seq. number	The atoms are supported with labels identifying their sequence number;

Type	The atoms are supported with labels identifying their type (H, C,  Cl, etc);

Type+number	The atoms are supported with labels identifying their type and sequence number;

Type+number in group	The atoms are supported with labels identifying their type and sequence number in groups of the atom type;

Clear labels	All labels on atoms are removed;

Labels style	Changes the default appearance of labels on atoms (size, font, etc).

Structural parameters	These subitems allow geometrical parameters in current structure to be viewed:

Show all interatomic distances	The distances between all atoms in selected fragment or the whole molecule are shown on the image. To hide them, right-click on the screen;

Show all bond lengths	The distances between bonded atoms in the selected fragment or the whole molecule are shown;

Show all bond angles	All bond angles in the selected fragment or the whole molecule are shown;

Clear	Clears all parameters designations;

Style	Allows the default appearance of lines and labels which represent structural parameters to be changed.

Show Van-Der-Waals spheres	Transparent spheres with sizes corresponding to standard Van-Der-Waals radii are drawn around all atoms (this feature is limited in the current version);

Toolbars	Displays or hides the toolbars on the main window.


Display menu

This menu allows the display scheme to be selected and edited. A scheme represents a set of parameters which affect the appearance of molecular structures on the screen: lighting parameters, colors of atoms and bonds, etc. One can select a scheme from the current set by clicking corresponding items of this menu. The last item "Customize" opens a window which allows new schemes to be added to the set, remove existing ones, or change the properties of each scheme.


Tools menu

Console Editor	Opens the Console Editor window to make complex geometry modifications;

Data Explorer	Shows the Data Explorer window, which represents all data read from an output file (this window is shown automatically when opening a new log file);

Build Z-matrix	Allows one to obtain a Z-matrix for the input file by clicking atoms in the molecule and specifying some additional information (see Z-matrix Builder for details);

GED tools	These subitems can be useful in Gas Electron Diffraction:

   Group distances in molecule:	Calculates all interatomic distances in the current structure and groups them by distance values with specified threshold convergence;

   Enumerate internal coordinates	Shows internal coordinates in the molecule, based on the atoms bonding (bond lengths, bond angles, dihedrals);

Crystallography tools/	These subitems allow the conversion of crystallographic fractional coordinates into Cartesian, and vice versa  (see Conversion between fractional and Cartesian coordinates);

Show parameters table	Shows a table representing structural parameters of the current molecule and vibrational frequencies;

Create input file	Opens a dialog box which automatically generates sections of input file with non-standard basis sets;

Orbitals	These subitems can be activated when a file with molecular orbitals is opened:

   Render molecular orbitals	Allows molecular orbitals read from the file to be visualized in the form of isosurfaces or colored figures;

   Analyze molecular orbitals	Shows a window with analysis of orbitals read from the file. At the moment this analysis is very simple and not well-elaborated. In future versions of the program the analysis will probably be improved and possibly become based on calculation of overlap integrals;

   Convert orbitals into input form.	These subitems allow molecular orbitals to be saved in text format, for use in an input file as an initial guess for new computation;

Supporting...	These subitems allow internal program settings to be modified, for example tables of standard bond lengths used in automatic bonds identification can be altered:

   Edit fragments database	Shows the Fragments Editor window to view and edit the standard set of molecular fragments (see Working with molecular fragments);

   Update possible bond len. table	Updates tables of bond lengths using the bonding in the current molecule. This options can be useful if automatic bonds identification works incorrectly for some of your molecules. Before using this button you should manually set all bonds in molecule (using Ctrl+B), not missing any bond. The new bonds data is immediately saved  to "bonds.bin" file. This utility in not implemented very well in the current version;

Associate file types	Allows ChemCraft to be registered as a program for viewing certain types of files (.out, .xyz). When ChemCraft is registered, these files can be opened immediately in Explorer or another shell.

Preferences	Allows the current settings of the program to be changed (see Preferences Window).


Obtaining isosurfaces of properties other than molecular orbitals

At the moment only cubes of molecular orbitals can be built from output/checkpoint files using ChemCraft. Properties such as electrostatic potential, total electron density, etc can be visualized in the following way:

For Gaussian users: cubes of different values can be built using the cubegen.exe utility distributed with Gaussian. To use this possibility one should do the following:

-	Obtain a checkpoint file (.chk), specifying %CHK in input file;

-	Convert it into formatted checkpoint file (.fch) using formchk.exe utility distributed with Gaussian (ChemCraft can automatically run this utility when opening checkpoint files);

-	Launch cubegen.exe utility specifying the name of the .fch file. The input options of cubegen are documented in Gaussian Help file;

-	Open the obtained cube with ChemCraft and use "Show isosurface" or other option.

For GAMESS users: at the moment we can only suggest using other programs which support visualization of such properties (e.g. Molden).