Spartan 5.1 User's Guide

Chapter 4: The File Menu

This section reviews the features and functions available under the File menu.

Selection of File results in display of the following menu:

New Ctrl+N
Open Ctrl+O
Close
Save
Save As
Merge As
Group As
Delete

Import
Export

Print Ctrl+P

Quit Ctrl+Q

(Keystroke equivalents are given by the letter underlined in the menu entry.)


Section 4.1: New

Enters the builder (for a discussion of builder functions, see Section 7.1). The builder may also be entered from Edit Structure under the Build menu with an existing structure (see Section 7.1).


Section 4.2: Open

Opens a file which contains all information associated with a particular molecule or particular list of molecules. Displays a structure model, or in the case of a list, displays a structure model for the first member of the list.

A dialog appears following selection of Open.

At the top is the Directory menu which provides the path to the current working directory ("interest_molecules/" in the example above). The body of the dialog is a list of files in the selected directory, i.e., a "file browser". These are either Spartan molecule files (themselves directories which contain all the files associated with a particular molecule), or additional directories going further down the tree. The latter are identified by a trailing "/". Spartan molecule directories may involve a single molecule or a list of molecules, the latter being identified by an "*" following the name.

A molecule (or list of molecules) may be opened in one of four ways: entering the molecule name in the box at the bottom of the dialog followed by clicking on Open, clicking on the entry followed by clicking on Open, double clicking on the entry, or positioning the cursor over the entry, pressing the middle mouse button, dragging the mouse out of the dialog and onto Spartan's main screen and finally releasing the button. The last of these, or "drag and drop" mode as it is termed, allows several molecules (or lists of molecules) to be opened with a single access to Open. The other three modes permit only a single molecule (or a single list of molecules) to be opened per access, i.e., the dialog is closed. Because drag and drop does not close the dialog, this must be done either by opening the "final molecule" in one of the first three modes, or by clicking on Cancel.


Section 4.3: Close

Closes the selected molecule. Removes the structure model and any graphical surfaces and/or slices from the screen.

If the active molecule was a member of a list, closes all the molecules in the list and removes the associated spreadsheet.


Section 4.4: Save

Saves the selected molecule exactly as it appears on screen, that is rendered in terms of a specific structure model, and (optionally) with one or more graphical surfaces and/or slices, and (optionally) vibrating along a specific normal mode. Opening the molecule will bring it on screen exactly as it was last saved. Save does not lead to any further requests, or informative dialogs, or to changes in the main screen.

Save is particularly useful for storing predefined information for later display, as for example, in creating a "slide show".


Section 4.5: Save As

Saves the current information being displayed. Upon selection of Save As, the user is provided with a file browser, and must supply a name, which if it already appears in the working directory, will cause a warning that pre-existing information is to be overwritten.

Clicking on Overwrite overwrites the information and exits the browser; clicking on Cancel returns to the file browser allowing the user to select another name. Once a file name has been supplied, clicking on Save saves the information and exits the dialog. The file on screen is renamed and the original file is closed. Clicking on Cancel exits the browser without saving the file.

Save As invoked for a member of a list saves the entire list. A single member of a list may be saved using Merge As (Section 4.6), and one or more members may be saved using Group As (Section 4.7). The best way to save one or more members of a list is to use Extract As under the Molecule menu in the spreadsheet (see Section 11.2.2).


Section 4.6: Merge As

Merges the coordinate files of all molecules presently displayed on screen into a single file. Upon selection of Merge As, the user is provided with a file browser, and must supply a name for the merged information which is to be saved. If the name supplied already appears in the working directory, the user will be warned that pre-existing information is to be overwritten. Clicking on Overwrite overwrites the information and exits the browser; clicking on Cancel returns to the file browser allowing the user to select another name. Once an appropriate file name has been supplied, clicking on Merge merges the coordinates into a single file and then exits the browser. Any files that were on the screen prior to selection of Merge As are closed, and what remains is a single file (and structure) representing the merged coordinates. This file is then treated as any other Spartan file, and has access to the full range of functions, including the builder. Clicking on Cancel exits the browser without merging the files. The original files on screen are unaffected.

In the situation where there is only one molecule on screen, Merge As behaves as Save As to save (copy) this molecule. This gives the ability to extract a single molecule from a list. (Recall, that Save As saves the entire list of molecules; see Section 4.5.) A better way to extract one molecule from a list is provided by Extract As under the Molecule menu in the spreadsheet (see Section 11.2.2).

Merge As is useful for forming complexes from two or more molecules. Among other things, these may be used to represent "separated products" in intermolecular reactions for the purpose of guessing transition states with linear synchronous transit procedures (see Section 7.3 and especially Section 7.3.3). Molecular complex formation is greatly facilitated by 3D viewing (see Section 2.8).


Section 4.7: Group As

Collects all molecules presently displayed on screen into a list, which later allows operations to be set up and carried out in Spartan's spreadsheet. Upon selection of Group As, the user is presented with a file browser, and must supply a name for the group. If the name supplied already appears in the working directory, the user will be warned that pre-existing information is to be overwritten. Clicking on Overwrite overwrites the information and exits the browser; clicking on Cancel returns to the file browser allowing the user to select another name. Once an appropriate file name has been supplied, clicking on Group collects all molecules presently on screen into a single (named) list of molecules, and then exits the browser. The original (individual) files are not lost, but are closed. Upon exit, a single molecule is displayed (the first member of the list). Clicking on Cancel exits the browser without collecting the files into a list. The original files on screen are unaffected.

Because Group As (as Merge As) acts only on those molecules which are presently displayed on screen, it may be used to save one or more members of a list. Merge As provides another mechanism for saving only one molecule from a list (see Section 4.6). A better method is to use Extract As under the Molecule menu in the spreadsheet (see Section 11.2.2).


Section 4.8: Delete

Deletes a molecule or list of molecules from the file system. Two different modes of operation are available, depending on whether or not one or more molecules (lists) are presently open on screen. With one or more molecules open, Delete acts to delete the selected molecule. With no molecules (lists) open, selection of Delete leads to a file browser, and request for a file name. Double clicking on a file name, or clicking on the file name followed by clicking on Delete, leads to an on-screen message warning that all files associated with the particular molecule (or list of molecules) are to be deleted. Deletion occurs by clicking on Delete. Alternatively, clicking on Cancel exits the browser without molecule deletion.

Only one molecule (list) can be deleted with each access to Delete.


Section 4.9: Import

Read (imports) data files from other sources. These are then translated into Spartan's internal format making the data available for further calculations. Clicking on Import results in display of a dialog very much like the Open dialog. At the present time, the following file formats are supported:

  • Sybyl (MOL and MOL2)
  • MACROMODEL
  • Brookhaven Protein Data Bank (PDB)
  • FDAT (crystal structures)
  • Spartan Cartesian
  • Spartan Exchange Format (for SpartanView)
  • Spartan Collection Format (for SpartanView)

These are identified and, except for crystals, are automatically translated to Spartan's internal format. Attempts to import other (incompatible) file formats will lead to an error message.

Successful import of a molecule, other than a crystal, will give rise to a dialog.

Following removal by clicking on Continue, the usual file browser appears to request a name for the information which is to be saved. If the name supplied already appears in the current working directory, the user will be asked whether the pre-existing information is to be overwritten. Clicking on Overwrite overwrites the information and exits the browser; clicking on Cancel returns to the file browser allowing the user to select another name. Clicking on Save in this dialog saves the information and exits.

Successful import of a crystal will give rise to a different dialog.

In addition, the crystal unit cell will appear in the Work Area. The dialog is divided into three parts:

  1. Unit cell parameters and space group are identified at the top of the dialog. The space group is displayed using "International Notation". To the right of the name is a pull-down menu allowing one to display the space group using:

    1. The Full International symbol;
    2. The International symbol;
    3. The Schoenflies symbol;
    4. The Hermann Mauguin symbol; or
    5. The space group number.

    These may not be changed in the present implementation.

  2. The middle of the dialog is an "Extract Molecule" button. Clicking on this expands a molecule from the crystal. If hydrogens are missing, a new dialog appears.

    Clicking on "Add Hydrogens" or "No New Hydrogens" will result in the specified operation. If "Add Hydrogens" was chosen, a new dialog that describes the number of hydrogens added will appear.

    Next, if there can be more than one unique molecule in the crystal, another dialog appears.

    Clicking on a molecule (or on Select All) extracts the selected molecule from the crystal.

  3. The extent of unit cell expansion is specified at the bottom of the dialog (ranges of 0 <= (x,y,z) <= 1 correspond to the unit cell). These may be altered as desired--following which clicking on Apply expands the data.

    By default, when the "Apply" button is selected, atoms inside the given ranges are displayed while atoms outside are "clipped" (not shown). This is referred to as "Exact" clipping. There are two other modes:

    1. "Polyhedra", in which atoms outside the ranges are included if they can be used to complete polyhedra partially included within the ranges. This is useful when looking at inorganic crystals.

    2. "Valence", in which bonds existing in the selected range are terminated with hydrogens (open valencies).

Following removal of the Crystal Panel by Saving the structure (under the File menu), the usual file browser appears to request a name for the information which is to be saved. If the name supplied already appears in the current working directory, the user will be asked whether the pre-existing information is to be overwritten. Clicking on Overwrite overwrites the information and exits the browser; clicking on Cancel returns to the file browser allowing the user to select another name. Clicking on Save in this dialog saves the information and exits.

Once a structure has been imported and saved, it is treated as if it came from Spartan's builder. That is, it has access to the full range of functions in the interface (including the builder).


Section 4.10: Export

Writes (exports) coordinate files and (optionally) atomic charges from Spartan to other programs. Selection results in a dialog.

At the present time the following file formats are supported:

  • Sybyl (MOL and MOL2)
  • MACROMODEL
  • Brookhaven Protein Data Bank (PDB)
  • Virtual Reality Mark-up Language (VRML)
  • Spartan Exchange Format (for SpartanView)
  • Spartan Collection Format (for SpartanView)

The user must select one of these and then supply a name. Names of existing molecule directories are not allowed, and attempts to use them will result in a message.

Click on OK to remove the dialog, and select Export again with another name.

If one or more sets of atomic charges are available, another dialog will appear in response to clicking on Export (SYBYL MOL2 and MACROMODEL
file types only).

The user needs to select which, if any, set of charges (from among those which are actually available) is to be included.

In previous versions of Spartan, Import and Export functions applied to only single molecules and not to lists of molecules.* In this version of Spartan, lists can imported and exported using the Spartan Exhange and Collection file formats. A list can also be exported in VRML format, appearing as a single multi-frame VRML file.

The molecule (with charges) is exported by clicking on Export.

This dialog (or in the absence of charges, the dialog obtained originally upon selection of Export) may be exited with the molecule being exported by clicking on Cancel.


Section 4.11: Print

Prints whatever is presently displayed on screen (according to the specifications made in the last access to Print Setup; see Section 3.4).


Section 4.12: Quit

Exits Spartan, i.e., clears the screen and closes all files in any directories which are presently active. A warning message is presented to the user for confirmation.

After quitting, the user is returned to the Unix shell from which Spartan was started. To return to Spartan, type spartan.


Notes

    * SYBYL MULTIMOL2 files (for sets of jobs) may be imported into Spartan or exported out of Spartan using external programs "multimol2.in" and "multimol2.out" available on the distribution media. Consult these for information on their use.


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