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Methods, Problems and Solutions

Powder Diffraction Structure Solution Pathways

Solving an Organic Structure (Cimetidine - C 10 H 16 N6 S) from Powder Diffraction Data

Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]

[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]

[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]

This example uses example Cimetidine data from the EXPO software


If EXPO gives problems, another option is to treat this as a single crystal problem and run the various single crystal programs such as are available in the common single crystal suites (ORTEX, WinGX, Platon/System S and Crystals). These structure solving programs include sir92/sir97, shelxs86/shelxs97, dirdif and crunch.

Obtain the HKL file from the Le Bail fit (you can use the extra.hkl file generated by EXPO). Use Armel Le Bail's overlap software to process and convert the HKL file into Shelx format. You may also want to use overlap to remove reflections that are too overlapping. Though to start with, it might not hurt to use "all" the reflections.


In this example, we will use WinGX as an interface into Sir97, though we could use Platon/System S. Whatever takes your fancy.

Copy the HKL file into a directory and run WinGX Autostart and input the cell, molecular formula, number of formula units in the cell (use the rule of thumb of 18 cubic Angstroms for every non-Hydrogen atom - Volume = 1279 Anstroms cubed: (1279/18 gives 71 non-hydrogen atoms: 71 / 17 (non hydrogen atoms in the Cimetidine molecular formula) = 4.1. Thus a Z=4) and other subsidery information (including a dummy crystal colour and crystal size). It probably will not recognise the spacegroup so input this when given the unknown prompt.

WinGX Interface


Then select Solve, SIR-97, Run SIR-97. Sir97 will run and possibly solve the structure. However, if the following case, it lost the structure in the automatic recycling.

Sir97


The way to stop it losing the structure in the recycling is to manually give Sir97 a Recycle 0 command.

Then select Solve, SIR-97, Open SIR-97 file (you can only do this after running Sir97 once from WinGX so the initial starting Sir file is generated). After %FOURIER as a new line with Recycle 0 and save the file.

Edit the Sir97 file


Now select Solve, SIR-97, Run SIR-97 (when prompted, Use the existing Sir file (which we just edited)).

Sir97 Solves the Cimetidine structure

Either use the Sir97 interface - or the programs offered by WinGX to rename the atoms appopriately.


[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]

[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]

[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]

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