Diamond Version 5 User Manual: Structure files

Inserting structure data into a document

This article is about several ways to add one or more structure data sets into a new blank document or to add another structure data set(s) into an existing document.
- The Structure -> Insert From File... command enables you to add one or more structure data sets from one or more files.
- The Structure -> From Structure Type Database... command lets you add structure data from an inorganic structure type database.
- With the Structure -> New Structure command you can add structural parameters manually or from a structure template to an existing document.

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Inserting Structure Data from a File

Since Diamond supports using multiple structure data sets in one Diamond document (saved as "diamdoc" file), you can insert one or more structure data sets from one or more files into the active document. If you insert a single file and the file contains two or more data sets, you have the opportunity to select the data sets to go into the document or not.

This is done with the command Insert From File in the Structure menu.

At first this command opens the Insert Structure(s) From File(s) dialog, which is a modification of the common MS Windows file open dialog. To select two or more files, click the file names while holding down the Ctrl key. To select a block of files, click on the last file name, then, while holding down the Shift key, on the first file of the block. You can control the rank order of the selected files from the "File name" input line.

When you confirm and close this dialog with OK, the Insert From File Assistant will follow and guide you through the following steps.

The Insert From File Assistant enables you to insert one or more structure data sets from one or more files into the active document. If you insert just a single file, you will have the opportunity to filter out data sets, if the file contains two or more data sets.

After the Welcome page of the assistant, the page "Files and Formats shows you the results of the file format recognition and the number of data sets found. In our sample we opened the sample file "PCD-VxOy.cif" containing 20 structure data sets with binary V-O compounds from "Pearson's Crystal Data":

With the Next button you proceed to the next page where you define if and how to let Diamond create pictures for the inserted structure data sets. In our sample, we use choose the option to let Diamond create pictures automatically basing on Diamond's proposal from a check of the structural parameters. (The advantages of manual, assisted, and automatic picture creation are described in "Automatic vs. manual picture creation" and the following articles.)

After pressing Next and then Finish on the last page of the assistant you have the choice to select one or more data sets. (Please note that it is not possible to select data sets, if you chose multiple files in the first dialog "Insert Structure(s) From File(s).)

Insert Structures From File dialog

This dialog is opened after the Insert From File Assistant and enables you to select data sets out of a file containing multiple structure data sets.

The table lists the data sets. A data set will be inserted into the active document, if its corresponding checkmark is set. The columns can be configured by using the Settings push button, which opens the Structure Table Settings dialog where you can choose the columns to be displayed and which column to sort for.

The buttons Select and Unselect can be used to activate the check marks in the rows that are currently selected or to clear the checkmarks, rsp. To activate all check marks, click on the first row and press Shift+End key, then press the Select button.

Confirming this dialog with OK to initialize the actual insertion of the data sets and optional picture creation.

After the insertion of the structure data set(s), Diamond changes to Thumbnail Preview (unless done yet). Depending on the picture creation settings in the Insert From File Assistant, these pictures are blank, contain content, or are simply "dummies" reading "Click here to create picture". In our sample we advised Diamond to create picture proposals automatically:

Screenshot of Picture Thumbnails View of the sample document "PCD-V5O9-LT-1250105.diamdoc" with the structure data set (PCD number 1250105) already in the document plus the four inserted data sets. The automatic picture creation created unit cells with V-O bonds in a clinographic projection.

If you did not choose an automatic or assisted picture creation, you can later choose one of the commands Picture/Picture Creation Assistant, Picture/Create Proposed Picture, or from the Build/Building Schemes/Run Scheme sub-menu to create a structure picture for every selected picture thumbnail with the guidance of an assistant or with a pre-defined building scheme. (In case of dummy pictures you will be prompted to start a picture before.)

Besides this, you can of course go to normal picture view by clicking into one of the thumbnails and build up or change a picture manually.

Inserting structure data from a structure type database

Beneath the option to insert one or more structure data sets from a file, you can insert a structure data set from Diamond's Structure Type Database, using the command From Structure Type Database in the Structure menu. This structure type dataset will be inserted optionally with or without one or more associated ready-to-use pictures.

The structure type database is described in detail in the article "Database with inorganic structure types". This article also describes how to browse for a structure type and if to insert ready-to-use pictures or use a guided picture creation or start with a blank picture and build up the picture manually step-by-step.

Running the command Structure -> From Structure Type Database opens the Insert Structure From Type dialog.

Here we choose a previously accessed structure type: diopside. (To browse for another structure type, we would use the Browse button to open the Structure Type dialog.) For pictures, we choose the option Load structure picture(s) to start from a ready-to-use picture:

Inserting new structure data manually

You can also create another structure data set for an existing Diamond document by typing in the structure parameters manually or use a structure template and adjust the structural parameters. This is done with the command New Structure from the Structure menu, which opens the New Structure Assistantwhere you choose if to start from scratch or from a template and enter or change, rsp., the structural parameters on the subsequent pages of the assistant.

This is described in the article "Entering a new structure": "Adding another structure to a document".

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