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Description of the CCP1 GUI menus and Key bindings


Key Bindings

Left Mouse Button

  • Rotates image.
  • Toggle selection of an atom.
  • Clicking away from an atom will clear any selections.

Shift Left Mouse Button

  • Rotate the molecule about an axis pointing out from the middle of the screen towards the user.

Middle Mouse Button (on unix systems)

  • Move the molecule in the plane of the screen.

Right Mouse Button

  • Moving the mouse forwards (towards the screen) makes the molecule appear bigger, moving the mouse backwards shrinks it.
  • Clicking on an atom will give local geometry information for that atom.

Key Strokes

Key Result
fFit image to window
rReset View
pAtom Pick
sSurface Representations
wWireframe Representations

File Menu

File menu screenshot

Open

Clicking on the Open Menu opens up a dialog box that allows to you select the type of file from which to load a set of molecular coordinates, as shown below:

File menu screenshot

The drop-down menu at the bottom is used to filter which file formats are displayed. The different filters available are:

  • Molecules - this displays all files with the most commonly used extensions that are supported by the CCP1GUI, namely:
    • .xyz (XMol file format)
    • .pdb (Brookhaven Protein Databank)
    • .pun (GAMESS-UK punch file)
    • .c (ChemShell cartesian coordinates)
    • .crd (CHARMM (Chemistry at HARvard Molecular Mechanics))
    • .z (ChemShell Z-matrix file)
    • .cml (Chemical Markup Language)
    • .xml (XML)
    • .zmt (Z-matrix)
    • .gjf (Gaussian Input File)
    • .mol (Molecular Simulations, Cerius 2)
  • XYZ - only XMOL .xyz files.
  • PDB - only Protein Data Bank .pdb or .PDBfiles.
  • CML - only Chemical/Xtensible Markup Language .cml or .xml files.
  • Zmatrix - only zmatrix .zmt files.
  • GAMESS-UK Input - only GAMESS-UK .in input files.
  • Other Output - all files with a .out extension. Selecting a file with a .out extension will bring up a box allowing you to select the type of output that the file is.
  • Gaussian Output - Gaussian output files with a .gjf extension ( very limited support ).
  • All - list all files types.

Save As

  • Save the coordinates of the molecule to a text file. Supported formats are:
    • Punch File - cartesian coordinates .pun
    • PDB - Brookhaven Protein Databank .pdb
    • CML - Chemical Markup Language .cml
    • MSI - Molecular Simulations, Cerius 2 .msi
    • CHARMM - Chemistry at HARvard Molecular Mechanics coordinate file .crd
    • SHELX.RES - SHELX crystal structure determination program.res
    • Zmatrix - internal coordinates .zmt

New Molecule

  • Create a new molecule, (currently a single carbon with 4 attached X (i.e. unidentified) atoms) and open the editing tools panel.

Save Image

  • Save the graphical image in the main window to file out.jpg in the current working directory (the directory from which the GUI was started).

Open Calc

  • Opens a calculation window and restores the results of the chosen calculation (.clc) file.

Quit

  • Exit the GUI.

Edit Menu

Edit menu screenshot

Edit Coords

  • Opens the molecular coordinates editor on the chosen molecule. The coordinates editor is used for editing the atomic coordinates of the molecule in either Z-matrix or Cartesian form. For more help on the Coordinates Editor, click here.

Edit Grid

  • Dunno.

Connect

  • Determine the connectivity according to the parameters specified in Edit -> Options -> Connectivity. You will need to do this if you have loaded in a molecule in .pdb format.

Extend

  • Extend a periodic structure with more repeat units (periodic structures can be read in from ChemShell unit cell format).

Delete

  • Delete the specified molecule.

Editing Tools

  • Opens a window with tools for molecular editing (point and click) operations. More extensive help on the Editing Tools can be displayed by pressing F1 when the Editing Tools window is displayed or clicking here.

Select All

  • Selects all the atoms of the selected molecule.

Select by bonds

  • Select all the atoms that are part of this molecular fragment (i.e. are part of the same bonded network).

Select (dist to sel)

  • Select all atoms within a specified distance of the currently selected atom(s). On selecting this item, dialog box will appear that you can use to specify the distance in Angstroms.

Select (dist to point)

  • Select all atoms within a specified distance of a particular point. The origin of the grid used to specify the point is the centroid of all currently selected atoms or the centre of the screen if no atoms are selected. On selecting this item, dialog box will appear that you can use to specify the coordinates of the point and the distance in Angstroms.

Select (dist to point) + trim models

  • This functions exactly as Select (dist to point), except that, following the selection, all unselected atoms will be hidden ( to show the atoms again, use the Adjust Molecule View tool ).

Delete Selected Atoms

  • Delete all the selected atoms.

Delete Unselected Atoms

  • Delete all atoms that are not currently selected.

Options

  • Opens the Options panel, allowing adjustment of defaults and parameters relating to the behaviour of the GUI. More extensive help can be displayed by pressing F1 with this window displayed or clicking here.

View Menu

Viewing Molecules

The CCP1GUI has extremely powerful and highly customisable capabilities for viewing molecules and the data resulting from a calculation. There are essentially three types of representation that can be accessed from the view menu. These are listed below with a more detailed description following on.

  • Molecule View - the representation of the atoms and bonds within a molecule.
  • Scalar Data - the representation of data that is defined by its magnitude at a point in space (such as orbital vectors or electrostatic potential).
  • Vector Data - the representation of data that has both a magnitude and direction at a point in space (such as a charge density gradient).

Molecule View

Molecule View Menu screenshot

Molecule views are grouped together under the View Menu according to the molecule to which they belong. Selecting a particular molecule from the View Menu opens a drop-down menu that lists the following options:

Show/Hide Molecule View

  • This is used to show or hide a particular view of a molecule.

Adjust Molecule View

  • This is where the properties of a particular view can be changed. Selecting this option will cause a dialog box to appear with the options listed below (this help may also be displayed by pressing F1 when the window is displayed).

New Molecule View

  • This creates a new view object for the molecule. The view can then be adjusted by selecting the view from the menu and selecting 'Adjust Molecule View' as above.

Adjust Molecule View

The adjust molecule view tool changes the way that the molecular structure is displayed on the screen. The tool is displayed below:

Adjust Molecule View Tool screenshot

The available options are:

  • Wireframe - a simple representation of a molecule with the bonds represented as coloured lines connecting the individual atoms. From their midpoint to the end connected to an atom, the lines are coloured with the colour associated with that atom type.
    • Show bonds - toggle the display of the wireframe bonds.
    • Contacts - atoms that are not connected, but whose centres are within a certain distance of each other can be considered to be in contact. If two atoms are in contact, when the contacts button is selected, the two atoms will be connected by a white line. The contact distance can be specified in the Connectivity tab of the Edit -> Options menu.

  • Spheres - the balls of the conventional ball and stick representation of molecules. Spheres are drawn centred on the individual atoms, sized and coloured according to the atom type that they are associated with.
    • Show - toggle whether the spheres are shown or not.
    • Scale - change the relative sizes of the spheres.
    • Radii - toggle whether the reference radius for the spheres is the Covalent or Van der Waals radius.

  • Sticks - the sticks of the conventional ball and stickrepresentation of molecules. Cylinders are drawn representing the bonds connecting individual atoms.
    • Show - toggle whether the bonds are shown or not.
    • Radius - change the width of the bonds.
    • Colour - change the colour of the bonds (default is grey).

  • Labels - this displays labels identifying the individual atoms. The labels show the type of the atom, as well as a unique number identifying each atom.
    • Show - toggle whether the labels are shown or not.
    • Size - change the font size used for the labels.
    • Colour - change the colour of the labels.

  • Draw Selected Atoms Only - only display those atoms that have been selected by clicking on them with the mouse.
  • Draw All Atoms - display all atoms regardless of whether they have been selected or not.

  • Update - refresh the screen to show any changed options.
  • Show - display the structure.
  • Hide - hide the structure.
  • Destroy - destroy this representation of the structure.

Scalar data view

Scalar View Menu screenshot

When a calculation is carried out on a molecule, the result is often returned as the value of the property (such as the charge density) mapped onto a 3-dimensional grid of points.

The GUI is equipped with a number of highly configurable visualisers for such scalar data on a grids. The following menu items list the visualisers and which of their properties can be adjusted. As the visualisers share many of the same tools, there are also links to explanations of what the individual property adjustment tools do

Density View

  • This defines a single isosurface for a specified positive value of the grid. The contour height is adjustable, as is the colour and opacity. The outline of the grid is also configurable.

Density Volume Visualisation View

  • In this view, a whole volume of space is coloured according to the value of the property within that volume. A transfer function can be selected and the outline of the grid is also configurable.

Orbital Volume Visualisation View

  • As for a density volume view, a whole volume of space is coloured according to the value of the property within that volume. A transfer function can be selected and the outline of the grid is also configurable. The difference between a density and orbital view is that, the density view expects the values to be in a range from 0 to a positive number, whereas the orbital view expects to colour the volume according to whether the values are positive, negative or zero.

Orbital View

  • This is similar to density view, except that a pair of isosurfaces are drawn, one for a specified positive value and another for the corresponding negative value. The colours of both of the surfaces may be selected.

Coloured Surface

  • The coloured isosurface representation creates an isosurface at a specified contour height. The colour, contour height, and opacity can all be configured. This surface can also be colour mapped according to the value of another property.

Grid View

  • This is the closest view to the 'raw' data and consists of a grid of points with their associated values. The size of the points on the screen can be altered as can their opacity and the colour mapping.

Cut Slice View

  • The cut slice view creates a 2-dimensional 'canvas' that can be moved through the molecule, with the values of the function at the point the slice is taken displayed on the canvas as contours or a colourmap. The size, orientation and position of the slice can be specified by using the Tran, Rot and Scale tools, which alter the position, orientation and size respectively, of the grid components. The density of points, or mesh, that the colour map or contours are mapped along any particular axis can be specified with the nx, ny and nz tools.

    The two tools at the top of the widget allow the opacity of the whole slice to be selected and also the colour of the border to be determined

    The options in the representations box determine which of the properties area shown.

    • If contours is selected, contours are displayed. The maximum and minimum contour values, as well as the total number of contours displayed can be specified with the Min Contour Height,Max Contour Height and Number of Contour tools. The tools in the Contour Colour Mapping group allow a colour map may also be defined for the contours.
    • If Colourmap is selected a colour map will be applied to the whole canvas as specified in the colourmap colour mapping group.
    • The border around the slice can be toggled on and off with the border tool.
    • An optional 2D-representation of the canvas can also be created in a separate window by selecting the 2D Representation. Selecting this option opens up a separate window displaying a face-on of the canvas, which can be saved to the current directory as the file out2d.jpeg.

Vector data view

Vector View Menu screenshot

Vector data is data that has both a magnitude and a direction at a point in space. The GUI's vector visualiser is described below.

Vector Visualisation

  • There are three ways that the GUI can visualise vectors:

    • Hedgehog Plot - this displays the vector as a line oriented along the vector. The length of the line is proportional to the magnitude of the vector. The lengths of the the hedgehog lines can be scaled with the scale tool, and the display tool toggles whether the hedgehog plot is displayed or not.
    • Oriented Glyph - this is similar to the hedgehog plot, but instead of lines, cones are drawn, with the orientation of the cone corresponding to the direction of the vector and the size of the cone proportional to the magnitude of the vector.

    • Streamlines - Streamlines can be thought of as the paths of particles that is travelling along the vector field. Starting at the point on the grid defining the vector, the particle moves forward a distance specified by the Integ Step Length and Step Length tools. At that point, the magnitude and direction of the new vector field is determined and the particle moves forward again in the new direction.

      The Propagation Time determines how long the particle will travel for, and hence how long the streamlines will be.

      The Display determines whether the streamlines will be displayed as lines, tubes or surfaces.

      The Integrate tool determines whether the particle will move forwards in the direction the vector is pointing, backwards, or whether the path will be traced in both directions.

      Computer Health Warning!: computing streamlines with Python code is extremely cpu and memory hungry and has been know to bring even the hardiest of Linux boxes to its knees!

  • All of the different vector views can have their colour mapping changed according to other properties with the Colour Map tool.
  • As displaying all of the points of the vector field is often not particularly information, the Sampling Grid tool can be used to select which points will be visualised. All of the points can be selected, or a 2-dimensional plane can be selected, or the points may be sampled according to another grid such as the grid defining the HOMO.

An explanation of the individual view properties:

  • Edit Colours - for surfaces that only have a single colour mapped to them, clicking on this option brings up the below dialog box that can be used to select the colour. The colour can be selected either by dragging the sliders to mix in various Red Green and Blue components, or the hexadecimal value of the colour can be entered in the selection box.

  • Colour Mapping - two or three elements of the colour map are configurable depending on the tool that it is being used in:
  • Colour Map
Tool screenshot

    • Scheme - this determines how the colours change as the value of the property that is being coloured changes from its minimum to its maximum value.
    • Lo and Hi - this determines the maximum and minimum values of the property that the colour spectrum will be mapped to
    • Colour By - for certain colour maps, this determines which property the colour map is describing.
  • Opacity - this determines how see-through the coloured surface will be.
  • Contour Height - this is the point value that the surface or contour will be mapped to; this effectively creates an isosurface mapped to the value specified in the contour height box.
  • Outline - this is just a line drawn around the outer edge of the 3-dimensional grid that the points are mapped onto. It's display can be toggled on or off, and it's colour specified when displayed.
  • Colour Field - this applies to the coloured isosurface tool, and colours the isosurface according to the property specified here. For example, an isosurface of the electron density can be displayed and this can be then coloured according to the electrostatic potential.
  • Transfer Function - A transfer function is used to colour individual volumes of space according to the value of a particular property within that volume. A transfer function is defined by a number of steps; each step is defined by an upper and lower value. If the value of the property within a volume of space falls within one of the steps, that volume of space is coloured according to the colour that has been ascribed to that step. The opacity of the volume can also be specified, so that the whole volume can be viewed at one time.
    • Vibrations

      If the one of the Frequencies options (finite difference or analytic) have been selected from the Properties Tab in the GAMESS-UK widget, then the vibrational frequencies of the molecule will be calculated, and the individual frequencies listed under the Views menu. To view a vibration, select the vibration from the views menu and a dialog box like the one below will be displayed:

      View
Vibrations Tool image

      The first few tools are the same as those for the Adjust Molecule View Tool. The additional vibration-specific tools are contained in the Animation box. These are:

      • Start - animate the selected vibration.
      • Stop - stop the animation.
      • Number of Frames - this is the number of still images that will be concatenated to create the animation.
      • Amplitude - this determines the size of the vibration: the distance from the equilibrium point of the vibration to its apex.
      • Frame Delay - the time-step between each frame that is concatenated to create the animation.

      Animation...

      • The animation tool brings up a set of controls that can be used to display a movie by cycling through the sequence of images that have been loaded into the CCP1GUI. There are buttons to 'play' the sequence in a loop, go to the first or last frame, or move forward or backwards a frame at a time. The animation tools are displayed below:

      View
Menu Animate Tool image

      • The animation tool is particularly useful if you have carried out a geometry optimisation under GAMESS-UK, as the geometry of the molecule at each stage of the optimisation is saved to the punch file. Using the animation tools, a movie showing the progression of the geometry optimisation can be displayed.

      Show/Hide All

      • Show All and Hide All affect the visibility of all graphical representations.

      Centre on Selected

      • Changes the origin for viewing and rotations of the centroid of the selected atoms.

      Info Menu

      Info menu screenshot

      • The info menu brings up a list of options to for displaying select information about the molecule. The information will be displayed in a pop-up window. Available options are:

        • Coordinate List - a list of all the coordinates of the atoms within the selected molecule.
        • Bond Length and Angles - a list of all bond lengths and angles for the selected molecule.
        • Contacts to Selected Atoms - a list of all the atoms that are close enough to be considered in contact with the selected atoms.

      Compute Menu

      Compute menu screenshot

      • The compute menu is used to select a program with which to run a calculation on the molecule. Currently, the GUI has control interfaces for ChemShell, Dalton, GAMESS-UK, MNDO and Mopac. For help relating to the control window for a particular program, press F1 when the window is displayed.

      Shell Menu

      Shell menu screenshot

      • The Shell menu is used to open an IDLE (Integrated Development Environment) Python shell - assuming you have IDLE installed. IDLE is included with most Python distributions, but if for any reason you don't have it, it is available from: http://www.python.org/idle
      • When opened from within the GUI, IDLE provides a powerful tool with which to interact with the GUI. The GUI Python objects can be operated on directly and information about them displayed.
      • It is also possible to write and run scripts to carry out complex operations.
      • More help on this is to follow.

      The Editing Tools Window

      Edit Tools screenshot 1

      Changing the element type

      • When it is first displayed, the upper half of the panel displays a selection of elements from the periodic table. To change the element type of an atom in the main window, select the atom with the mouse (so that a yellow square appears over it) and then click on the button representing the element type you would like the atom to be changed to.
      • If the element you are after isn't displayed in the selection, click on the 'More...' button to display a full periodic table. To shrink the window back down so that it only displays a small selection of elements, click on the 'Short Table' button.

      Edit Tools
screenshot2

      Editing

      The tools in the Editing Group perform a number of simple editing operations on a molecule, namely:

      • Del Atom - deletes the selected atom(s).
      • Del Bond - deletes a bond between two ( and only two ) selected atoms.
      • Add Bond - creates a bond between two selected atoms.
      • All X->H - when a new molecule is created ( using File -> New Molecule ) or new atoms are added to the molecule, the atoms at the end of the bonds are created as generic "X" atoms. This button converts all the "X" to hydrogen atoms.

      Hybridisation

      The tools in the hybridisation group change the hybridisation of the selected atoms. If you click on an atom that is only connected to a molecule with a single bond, changing the hybridisation scheme will add however many generic atoms your hybridisation scheme permits. You may then change their type individually or convert them all to hydrogens as described above. Various hybridisation schemes are available:

      • sp   =  sp
      • sp2  =  sp2
      • sp3  =  sp3
      • tpy  =  trigonal pyrimidal
      • sqpl =  square planar
      • sqpy =  square pyramidal
      • oct  =  octahedral

      Add Fragment

      To speed up the construction of large molecules, the GUI supports the ability to add molecular fragments to a given atom. To add a molecular fragment, select the atom to which you would like to add the fragment in the main window, select the desired fragment from menu on the right hand side of the Add Fragment frame in the Tools window and then click Add. Supported molecular fragments are:

      • Me   =   methyl
      • Pr  =  propyl
      • t-Bu  =   tertiary butyl
      • CO  =   carbon monoxide
      • Bu =  butyl
      • eta Bz =  η (π-bound) benzyl
      • eta Cp  =  η (π-bound) cyclopentadienyl
      • i-Bu  =  iso butyl
      • eta Ethylene  =  η (π-bound) Ethylene
      • i-Pr  =  iso propyl
      • Et  =   ethyl
      • Py  =  phenyl

      Measure

      The tools in the Measure group provide a quick way to determine the various properties for selected atoms. The value of the property for the selected atoms ( which are identified by their number ) is displayed in the space to the right of the buttons in the group.

      • Distance - the distance ( in Angstroms ) between two selected atoms.
      • Angle - the angle ( in degrees ) between three selected atoms.
      • Torsion - the torsion ( or dihedral ) angle defined for 4 selected atoms ( 1-2-3-4 ), is the angle between the planes defined by atoms 1-2-3 and the plane defined by atoms 2-3-4.

      Clean

      The tools in the Clean group provide a quick way to run a geometry optimisation to "clean up" a molecular structure. The ability to use these tools depend on the relevant codes to perform the optimisation being installed, as the CCP1GUI currently does not have the ability to run an optimisation internally. The options for cleaning are:

      • Clean - this runs the geometry optimisation and replaces the structure in the window with the optimised structure.
      • The second menu option is used to select the code with which to perform the geometry optimisation. Supported codes are:
        • Mopac - use the Mopac. Mopac is freely available from the WebMo website or from the CCL website.
        • MNDO - use the MNDO code.
        • UFF - use the UFF forcefield code.
        • GAMESS-UK - use GAMESS-UK.
      • Opts... - clicking on this button will bring up a menu for configuring how the geometry optimisation will be performed with the selected code.

      Return to the Edit Menu


    Edit Options Menu

    Files

    Edit Options File screenshot

    • At present, there are no editable attributes available here.

    Connectivity

    Edit Options Connect screenshot

    • Connection Parameters

      The parameters here determine how the gui decides if two atoms are bonded (assuming that the connectivity has not been specified in the input file). The formula that is used to determine bonding is:

      rij < scale * (rcov(i) + rcov(j)) + tolerance

      where rij is the distance between the two atomic centres, rcov(n) the Van der Waals radius of the atom, scale the radius scale factor and tolerance the tolerance.

      • Radius scale - this determines the radius scale in the above formula.
      • Tolerance - this determines the tolerance in the above formula.
    • Non-bonded Connection Parameters

      The parameters here determine how the gui decides if two non-bonded, but adjacent atoms, are in contact with each other. This determined using the same formula as for bonded atoms and the same parameters are adjustable.

    Visualisation

    Edit Options Visualisation screenshot

    The visualisation options here permit the user to define exactly how the GUI will represent the various objects that it draws.

    • Pick Tolerance - this allows you to change how close you have to place the mouse pointer to an object in order to be able to select that object.
    • Background Colour - clicking on the 'Choose' button will bring up an colour editing widget to change the background colour of the GUI.
    • Clipping Planes - this determines at what point VTK ( the underlying graphics toolkit ) will stop trying to display objects depending on how near or far away from the "camera" they are. This should be left at Auto unless you know what you are doing or are _really_ bored...
      • Near - distance to the front clipping plane
      • Far - distance to the back clipping plane.
    • Molecule Line Drawing Settings - settings here can be used to change how the molecules appear when they are drawn as lines ( i.e. when they are not being displayed as spheres ).
      • Line Width - the width of the line used to draw the molecules.
      • Point Size - the pint size of the line used to draw the molecules
    • Sphere Properties - the features here can be used to tweak how the spheres appear on the screen.
      • Resolution -
      • Specular Power -
      • Diffuse -
      • Ambient -
      • Specular -
    • Cylinder Properties- the features here can be used to tweak how the cylinders appear on the screen
      • Resolution -
      • Specular Power -
      • Diffuse -
      • Ambient -
      • Specular -
    • Data Line Settings -
      • Line Width -
      • Point Size -

    Developmental

    • At present, there are no editable attributes available here. The Editing Tool Panel is used to change various properties of the molecule displayed in the main window.

    Return to the Edit Menu


    The Edit Coordinates Window

    ZME screenshot
    • This can be used to manually edit the coordinates of the atoms in a molecule using either internal (displayed as a Z-matrix) or Cartesian coordinates. It is also possible to mix and match the two.
    • The coordinates window at the top of the Edit Window is a table displaying the coordinates. Each row corresponds to an individual atom. The table below shows the meaning of each of the columns in this panel for Z-matrix format and Cartesian coordinates.

    Title Cartesian Zmatrix
    i A number serving as a unique identifier for the atom Same as for Cartesians.
    Sym The chemical Symbol for the atom - a number may be appended to this to help identify the atom. Same as for Cartesians.
    i1 Unused The first atom to which this atom is connected.
    x/r The x-coordinate of the atom in Angstroms The distance of this atom from the atom specified in i1.
    i2 UnusedThe second atom to which this atom is connected.
    y/theta The y-coordinate of the atom in Angstroms The angle between this atom and the atoms identified in columns i1 and i2.
    i3 UnusedThe third atom to which this atom is connected.
    z/phi The z-coordinate of the atom in Angstroms. The dihedral angle between this atom and those identified in the fields 1i,i2 and i3.
    connections The other atoms to which this atom is connected. Unused

    Input Line

    • Values in the coordinates window cannot be edited by directly. However, by clicking on the row corresponding to an atom in the coordinates window (or clicking on the atom in the main window), the values for that atom appear in the Input Line fields headed "Enter Coordinate values" that sits below the table. By clicking in a field, the value can then be edited.

    Variables

    • The Variables field shows any values that are specified as variable within the coordinates window.

    Error Output

    • If there is a problem with any of the coordinates that have been entered, an error message will be displayed here.

    File Menu

    Save Zmatrix

    • Save the coordinates to a simple text file with the extension .zmt

    Load Zmatrix

    • Load coordinates from a file.

    Reload from Graphics Window

    • Update the coordinates window with the coordinates from the molecule displayed in the main window.

    Edit Menu

    Select All Atoms

    • This selects and highlights all of the atoms specified in the coordinates window  - the corresponding atoms in the main window will also be highlighted.

    Insert Atoms

    • This opens up a blank Input Line so that the coordinates for a new atom can be added.

    Copy Atoms

    • The values for the specified atoms will be copied into a buffer ready for pasting.

    Cut Atoms

    • The atoms will be removed from the coordinates window, but the values will be copied into a buffer ready to be pasted.

    Paste Atoms

    • Paste the coordinates of any atoms that were saved into the buffer into the table.

    Delete Atoms

    • Delete the selected atoms, but don't save their values.

    r,x -> var

    • Specify the value for x-coordinate or r as a variable (this value will then be displayed in the 'Variables' window).

    theta,y -> var

    • Specify the value for y-coordinate or theta as a variable (this value will then be displayed in the 'Variables' window).

    phi,z -> var

    • Specify the value for z-coordinate or phi as a variable (this value will then be displayed in the 'Variables' window).

    all -> var

    • Specify that all the selected values should be variables.

    Select All Variables

    • This selects all of the variables displayed in the 'Variables' window.

    Delete Variables

    • Remove a value from the variables window and specify it as a constant.

    Convert Menu

    Reorder Atoms

    • Not active at present

    AutoZ

    • Not active at present.

    Convert Selection to Z-Matrix

    • Convert a selection displayed as Cartesian to be displayed in Z-matrix form.

    Convert Selection to Cartesian

    • Convert a selection displayed as Z-matrix to be display in Cartesian form.

    Calculate Menu

    Auto Recalc

    • This toggles whether the coordinates should be recalculated as each change is made or whether the calculation should wait until 'Recompute Now' is selected.

    Recompute Now

    • Recompute the Z-matrix.

    Return to the Edit Menu

Return to the CCP1GUI homepage

 
 
   
 
For more information about the work of the Computational Chemistry Group please contact Paul Sherwood p.sherwood@dl.ac.uk or Bill Smith w.smith@dl.ac.uk
 
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