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Tutorials and Examples

Automated Single Crystal Structure Solution Using Sir2002

Example of solving a large organic structure with Sir2002

The CCP14 Homepage is at http://www.ccp14.ac.uk
[CCP14 Tutorials page] | [Sir97/2002 Tutorial Index] | [EXPO]
[WinGX] | [Crystals] | [Platon/System S]

Sir97 (and soon for Sir2002) can be spawned transparently from the following single crystal suites (freely available for students and academics) :

Warning: if trying to solve large structures using Sir2002 on MS-Windows operating systems, a personal opinion is that it would be best to have a separate "number crunching" PC to run the Sir2002 jobs. Sir2002 can take many hours to a few days to solve on large problematic structures, and running other programs on the PC can make things very sluggish, and cause Sir2002 to fail due to lack of memory. Windows (despite the official hype) - is not really up to this type of multi-tasking

Note: a feature of Sir97 and Sir2002 that may not be obvious is that if it fails to solve on the first trial, you should just leave it run. Sir2002 by default goes through the first 200 Trials.

The following example structure is a large cyclodextrin. On a 800 MHz Pentium PC running Windows 95, takes a few days to solve (it solves on Trial 132).

Be wary that Sir2002 assumes you have put in the correct chemistry (or close to the correct chemistry). When in doubt, perform an elemental analysis. It is not that uncommon for other elements to be present in inorganic crystals, especially if a flux of different composition has been used to grow the crystals.

Obtaining the data

Click here to obtain the 2 Meg zipped hkl data and Sir2002 starting file. Be wary that on default mode, this data can take 1 to 2 days to solve on a fast PC.

First method of starting out with Sir2002

Copy over an existing Sir2002 *.sir file. Open the file in your favourite text editor and modify the cell, hkl file, spacegroup and contents information as per the following. By default, Sir2002 assumes F-square data. While the "Fosquare" command used in Sir97 is now redundant in Sir2002, it will not cause any harm having it in. 
%window
%structure    sadf
%init
%job   sadf in P 21 21 2
%data
Cell     29.420  29.891  30.686  90.000  90.000  90.000
Space   P 21 21 2
Content   C  1000 H   800 O   400
Reflections   sadf.hkl
Format  (3i4,2f8.2)
Fosquare
%continue

Second method of starting out with Sir2002

Run Sir2002, and from the top left menu select, File, New to give the following GUI screen. Enter the directory where the hkl data is located, then fill in the information that Sir2002 requires.

Run Sir2002 to bring up the following starting screen
From the top left menu select, File, Load and Go. Select the *.sir file and then select the Go ICON. You can edit the information before trying to solve the structure by selecting the Edit ICON.

Be Patient and let Sir2002 run to completion

If you want to break Sir2002 from running this job, you can click on the top right STOP icon (the Icon has a hand symbol)

Sir2002 solves on Trial 132

In this example, Sir2002 has solved the structure in default mode. If it does not, there are hints within the manual on what to try next. Select the top right Help menu for the HTML based help.

If Sir2002 solves on a high numbered trial, but you somehow stuff things up by playing around - there is a way to just resolve on a desired trial number, or a range of trial numbers.

Exporting a solved structure from Sir2002 into another format

Using the top menu, select File, Export and choose your desired file format. (Shelx, Caos, Crystals, Schakal, etc)

[CCP14 Tutorials page] | [Sir97/2002 Tutorial Index] | [EXPO]
[WinGX] | [Crystals] | [Platon/System S]
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