[sdpd] Tutorial on Solving an Organic Structure from Powder Diffraction Data

[L.M.D.Cranswick...@dl.ac.uk]

There is a new tutorial on the CCP14 site for 
Solving an Organic Structure from Powder Diffraction Data 
using freely available software (example using the pharmaceutical:
Cimetidine - C 10 H 16 N6 S) as a demonstration of what software is 
available to aid in this activity.
  
  http://www.ccp14.ac.uk/solution/powder_structure_solution_pathways/cimetidine.html

This includes custom tutorials showing particular software packages working
on Cimetidine - as well as links to available software.

===========

Custom Tutorials:

Initial Connectivity Searching of the Cambridge database for Cimetidine 
like molecules using CORINA, Platon and  Quest/CSD

Data conversion, peak profiling, indexing and spacegroup assignment:

   Profile the peaks using XFIT to profile and fit the Cimetidine data

   Powder Indexing to get the cell and spacegroup using the combination 
   of Crysfire and Chekcell for Windows

>From the obtained Cell, checking if the structure has been found already:
   Ton Spek's Platon as an interface to CELL Searching the Cambridge 
   database via Platon and Quest 

Le Bail fitting:
    Le Bail fitting and generating an EXPO starting file using LHPM-Rietica

Solving the Structure (conventional methods):

  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

  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 GUI WinORTEP

  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

Last Resort Slow Real Space Methods of Solving Structures from Powder 
Diffraction Data:
  
  Using the Le Bail fit HKL file to try and Solve the structure of 
  Cimetidine using Armel Le Bail's ESPOIR Monte Carlo Structure 
  solution software:
     a)  with no restraints
     b)  with bond legth restraints
     c)  defining the rigid part of the molecule as a fragment

Checking for missing symmetry/checking for related structures:
  
  Platon's Addsym to find possibly missing Symmetry in cimetidine 
  and possibly correctly assign the spacegroup based on the atom positions 
  
  Ton Spek's Platon as an interface to Quest and the Cambridge Structure 
  Database to search for related structures. 


Links to Data format interconversion, HKL file overlap processing and
interconversion, Rietveld refinement software, Photorealistic Rendoring of 
the Structure, Hydrogen Placement using Single Crystal Refinement 
Software, etc.

-- 
Lachlan M. D. Cranswick

Collaborative Computational Project No 14 (CCP14)
    for Single Crystal and Powder Diffraction
Daresbury Laboratory, Warrington, WA4 4AD U.K
Tel: +44-1925-603703  Fax: +44-1925-603124
E-mail: l.cranswick...@dl.ac.uk  Ext: 3703  Room C14
                           http://www.ccp14.ac.uk