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 the 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 bond energies (checkboxes "Show atomic properties", "Show bond properties"), dipole moment (checkbox "Show dipole moment"), graphs with IR, Raman or electronic 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, derived 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 the 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 log files the bonds are usually printed; by default, only bonds with bond order not less than 0.25 are shown in 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  (see Interface notes). Pressing Shift with Num1-Num9 slowly rotates/translates the molecule.

Working with molecular structures

            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 shown 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 the current parameter in 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  is pressed, the coordinates of only last selected atom will change; if the button  is pressed, first and last selected atoms will 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 ones via selecting pairs of atoms and pressing Ctrl+B. For additional details on such geometry modifications, see Constructing molecules.

            The Coord mode allows one to import or export coordinates of atoms in text format (in angstroms or Bohrs). When switching to this mode, the text with coordinates is refreshed according to current molecule; while 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 from the clipboard into the textbox. Pressing Paste twice automatically switches to the Image mode. The text is automatically refreshed for current molecule by pressing "Show sequence" or "Angstroms/Bohrs", so pressing these control keys can restore accidentally corrupted or replaced text.

            The "Edit/Drag atoms" menu item or button  allows the atoms in the molecule's image to be moved using the mouse. When dragging an atom one can move it in the Z direction (in parallel with the view) using the keys Num2/Num8 (while the left mouse button is pressed). The buttons , , switch between "drag atoms", "drag fragments" and "drag molecules" modes, the latter two modes allow one to drag and rotate groups of several atoms (for details, see Constructing molecules). When a group of atoms is dragged, the buttons Num1-Num9 rotate it or move it in the Z direction.

            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 new molecules to be 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 provide the transfer of fragments via clipboard (e.g., to copy a radical from one molecule to another).

            If you copy a radical fragment from one site to another, the first atom to select is that connected with the outer molecule. See Working with molecular fragments for more details.

Using molecule rendering possibilities:

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

            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 ,  and further. Chemcraft also allows additional labels and lines to be added to the picture of molecule from the "Auxiliary designations" panel, enabled by the button  (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 or 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, so that the orbitals and basis set information are printed in the 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 the 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 buttons "Keep this surface" and "Delete all" can be used to obtain multiple isosurfaces in 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 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 can be used as an initial guess for a new calculation ("Tools/Orbitals/Convert orbitals into input format/" menu items or "Tools/Convert orbitals into input format" items in Data Explorer at the left).

            Chemcraft can convert fractional coordinates, used in crystallographic measurements, into Cartesian ones. 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" allow a specified point group to be easily applied to the molecule, if its geometry is satisfactorily close to the required symmetry.

            Chemcraft can calculate root-mean-square distances between the Cartesian coordinates of two molecular structures ("Tools/RMS compare structures" menu item, see here). Besides that, the program can merge multiple structures to allow the user to visually see the difference between them.

            Chemcraft can create animations of vibrations, molecule rotation, scan jobs in the format of animated GIF files ("Tools/Create animation" menu items).  

            Chemcraft provides the possibility to make script files for running multiple jobs ("Tools/Scripts/" menu items).  

Additional remarks:

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

            If Chemcraft doesn't identify bonds in the molecule correctly, one can manually set all bonds via Ctrl+B (no bond should be missed), or choose "Tools/Chemcraft incorrectly..."..

            Chemcraft can correctly visualize incomplete calculations (e.g., unfinished optimization, scan jobs). The output files being computed can also be opened. Pressing Ctrl+R reopens last opened file.  

            For the output files with geometry optimization, scan jobs, often the molecular geometry is switched several times during the optimization. To avoid this problem, choose the Tools button at the left (the job node should be clicked firstly), then "Set common orientation for all geometries".

            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.

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