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Tutorials and Examples

ORTEX for Windows Single Crystal Suite by Patrick McArdle

User friendly finding of Voids in a crystal structure

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[Tutorials page] | [ORTEX Tutorial Index]

The latest ORTEX (24th February 2000) now has the option to find voids in a structure. Any Shelx file can be used and it is very user-friendly operation. If Void finds some voids, it can add these as dummy atoms into the Shelx file to assist in visualisation.

The following uses the Tetracycline Hydrochloride structure as an example.

In the ORTEX directory, run Oscail to bring up the following starting Window

Oscail Starting Screen

Click on the J (Job name) Icon and change the name of the jobname to tetcy. If not in the \ortex directory where the tetcy.ins file is located, click on the change directory icon and enter this directory. (in this case in the \ortex\tetcy directory)

Changing the Job Name

Click on the Run Job icon and then select Roinn 2 after which the option to run the Void program should be visible.

Prior to running Void

Select Void and run. When prompted with an options box for Void, going with the defaults should be OK for this example.

Running Void

Void will now present the unit-cell containing the structure.

Void with unit cell containing the structure

While it is possible to examine the structure in more detail with the various options. We will go straight to the Void determination which presents the following dialog box.

Void options box

We will go with the default. But first it might be wise to get an estimate of how much time this will take (in this case on a 166MHz Pentium laptop). Select Calculate CPU Time then OK. The time will appear at the top left of the screen.

Estimating Void Computation Time

As around 5 minutes does not seem that much of a problem, select Search then OK to start trying to find some Voids. Any voids found will be indicated on the screen as it occurs. A % complete bar will indicate how complete the search is. In the following case, no Voids of significance are found in the structure.

Finding Voids

Void atoms, if found, are given a different colour and there is the option of saving to the Shelx for viewing in other structure evaluation software.

As an example of Void finding voids, following is a Void search being conducted on a zeolite.

Void Search on a Zeolite

In the result, the blue atoms/balls mark found voids.

Void Search on a Zeolite

Selecting the Reduce menu option will then write a unique set of voids to the Shelx INS file as dummy atoms.

Void Search on a Zeolite

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