From the Cell, checking if the structure has been found already

• Ton Spek's Platon can then be used as an interface to CELL Searching the Cambridge database via Platon and Quest

Le Bail fitting for confirming cell/spacegroup and obtaining a single crystal like HKL file

• Use Le Bail extraction in an appropriate Rietveld package (or the latest Powder Cell software) to confirm that the obtained cell and spacegroup looks good using a whole profile structureless fit.
  • Le Bail fitting and generating an EXPO starting file using LHPM-Rietica

Solving the Structure

• Use EXPO (sequel to Sirpow): Solve the structure of Cimetidine using direct method structure solution from powder diffraction data using the Sirware EXPO program

• Using the Le Bail fit HKL file, WinGX and Sir97; treating this as a single crystal problem and Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software
  • Available Single Crystal Suites and structure solving software they link to:
  • WinGX for Windows (Shelxs 97/86, Dirdif 99.2, Sir92/97, Patsee)
  • ORTEX for Windows (Shelxs 97/86)
  • Crystals for Windows (Shelxs 97, Sir92/97)
  • Platon/System S for UNIX (Shelxs 97/86, Dirdif 99.2, Sir97, Crunch)

• Be wary that if a heavy atom was present (Sulphur or Chlorine counts as a heavy atom in many structure problems), it would also be possible to try Dirdif in its default Patterson mode. There is a Sulphur in this structure: thus it might be possible to use Dirdif Patty to solve the structure using automatic Patterson methods. Using WinGX for Windows or System S for UNIX, this can be attempted at the click of a button in the same way the above Sir97 tutorial has been done.

• Preparation for fragment searching (one method if there are no representative fragments from the Cambridge Database): Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3

• Using the Le Bail fit HKL file, WinGX/SXGRAPH and Dirdif; treating this as a single crystal problem and Solve the structure of Cimetidine using Dirdif fragment searching

Solving the Structure (part 2)

Last Resort Slow Real Space Methods of Solving Structures from Powder Diffraction Data

• Using the Le Bail fit HKL and Vincent Favre-Nicolin's FOX software (Free Objects for Xtallography) simulated annealing solution software. Read the FOX readme on solving Cimetidine from powder data
  • [FOX website | CCP14 UK Mirror | CCP14 Canadian Mirror | CCP14 US Mirror]

• Using the Le Bail fit HKL and Armel Le Bail's ESPOIR Monte Carlo Structure solution software:
  • Also refer to the tutorial by Armel Le Bail on "Setting up the program files in < 10 minutes" - example of solving on an organic - and also defining torsion angles:
    • http://sdpd.univ-lemans.fr/sdpd/espoir/10mn/
    • [French Mirror | CCP14 UK Mirror | CCP14 Canadian Mirror | CCP14 US Mirror]
    • Solve the structure of Cimetidine with no restraints

    • Solve the structure of Cimetidine with bond restraints

    • Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies and freely moving atoms

Solving the Structure (part 3)

• C2·Powder Solve and C2·Powder Fit by Accelrys
• Crystal Structure Determination Package (CSD)
• DASH
• DIFFRACplus TOPAS
• Endeavour Structure Solution from Powder Diffraction Software

Checking for missing symmetry/checking for related structures

• Ton Spek's Platon could then be used to validate/check the structure by doing such things as using:

  Platon's Addsym to find possibly missing Symmetry in cimetidine and possibly correctly assign the spacegroup based on the atom positions

• Also you can use Ton Spek's Platon as an interface to Quest and the Cambridge Structure Database to search for related structures.

Rietveld Structure Refinement

• The structure is then refined in the Rietveld package of personal choice.
  • Refer Rietveld packages listed in CCP14 Auto-Mirrored Web/FTP Sites

  • Refer Restrained Rietveld Structure Refinement of Organics

• It is possible that the structure has not been solved to completion. Thus you may need to go through fourier difference maps as part of the refinement process. Only some of the available Rietveld programs have access to Fourier map functionality.
  • Rietveld programs that have the ability to generate and view electron density Fourier Contour maps

Hydrogen Placement using Single Crystal Refinement Software

• WinGX for Windows (Including "GUI CALC OH", "GUI XHYDEX" and the soon to be released SXGRAPH) and Shelxl
  • Placing Calculated Hydrogens on Cimetidine Hydrogens using Shelxl97 via SXGRAPH and the WinGX Single Crystal Suite

• Crystals for Windows
  • Placing Calculated Hydrogens on Cimetidine using Crystals for Windows

• Platon/System S for UNIX

• CAOS/Sir97 for Windows, UNIX and VMS

• Overall: Packages to look for include, Shelxl, Sir97, CAOS, Crystals. (and Single Crystal suites such as WinGX, Platon, (Crystals again), ORTEX, Platon/System S)

Calculating a powder diffraction pattern from the structure

• Within Single Crystal Suites
  • WinGX for Windows (Shelxs 97/86, Dirdif 99.2, Sir92/97, Patsee)
  • ORTEX for Windows (Shelxs 97/86)
  • Platon for UNIX (Shelxs 97/86, Dirdif 99.2, Sir92/97, Crunch)

• Powder Cell for Windows

• Poudrix for Windows (part of the LMGP Suite)

Photorealistic Rendering of the Structure

• Many of the single crystal suites such as ORTEX, Powder Cell, System S/Platon and WinGX (which includes Ortep-3 and GUI WinSTRUPLO) also allow convenient structure visualisation and output; including photorealistic rendering and animation of the structure.
  • Available Software for Structure Drawing and Visualisation

  • ORTEX: Creating a photorealistically rendered movie at the click of a few buttons

  • Using WinGX to Create/Render Photo Realistic Crystal Structures
    • Refer: [Louis Farrugia ORTEP Gallery] | [CCP14 UK Mirror]