Example 8

Web tools enable Xtal to read and model CIF data automatically

Because the Xtal routine CIFIO can read and write files in CIF format, it is simple to generate CIFs for publication, or read and validate CIFs from other sources such as the CSD. This is important for communicating data between the increasing number of software packages, databases and journals that receive and supply data in CIF format. It is possible to use a Tcl/Tk script to link the Xtal System or RasMol to CIFs downloaded from databases or journals using the web browser Netscape The steps in this process are illustrated below.

Xtal can be used to view CIF's downloaded by Netscape via Tcl/Tk filter as a helper application.

When this filter is installed, clicking on the [CIF] URL in the left-hand corner of this Netscape display of a Acta C Contents page, will download the CIF of the shown structure. This process automatically opens up the CIF Filter window shown in the next image.

Clicking on the [Goto] button gives a menu of all of the datablock header names in the CIF, and dragging to any of these names moves the view pointer to the start of the datablock. For example, in the left hand window the data block "re2biphoac4" is highlighted in red.

Clicking on [data_re2biphoac4] invokes a popup menu permitting you to choose the desired viewing software to visualize the structural data stored in the "re2biphoac4" data block.

Selecting the [Xtal +tcl/tk] option brings up the Tcl/Tk XTAL Program Control Window. The adjacent image shows the default Xtal input control lines (top frame) and the output listing (bottom frame) of executed programs. Control lines can be executed individually or together. In this way graphics programs such as PIG and PREVUE can be run and used to display the structural model specified in the downloaded CIF.