SDPD Internet Course

Week 7

Structure solution by Patterson, direct or molecule location methods, part 2 :
Special methods (molecule location excluded).


This week will be dedicated to the use of [if available] special methods (excluding molecule location)...

We are now at the limits of knowledge and close to the most recent developments in SDPD. Literature is scarce on those "special methods". Some may have been applied to a quite small number of real problems, and sometimes to none. There are very few programs available in the public domain, see the list at the SDPD-Database (CD). Moreover, the commercial programs are sometimes extremely expensive. For instance PowderSolve/Materials studio from the Accelrys/MSI Company, was, at the beginning, only available to a consortium of the biggest pharmaceutical companies and to large scale facilities like ESRF. The cost of the entry ticket was of the order of 40000 US$ for 3 years. Such an investment is out of small labs possibilities. However, researchers which cannot access to those monsters, can try to build their own program. Fortunately, this is what happens sometimes, so that a few program under GPL (GNU Public License), with open sources, may be grabbed here and there. They may be able to produce the same result as those unavailable programs, but without any shiny GUI (Graphical User Interface), so that they are possibly harder to manage for non-crystallographers. But you are a crystallographer, don't you?

If you try to identify those special methods (CD) from the publication titles gathered inside the SDPD-Database, you will probably obtain the following list of methods, or names, as defined by the authors themselve :

  • Monte Carlo from scratch - 1999
  • Global Optimisation Method (GOM) - 1997
  • General Monte Carlo approach - 1997
  • Simulated-annealing method and a high degree of molecular flexibility - 1997
  • Optimised data collection and analysis strategies - 1997
  • Genetic algorithm - 1997
  • Anomalous scattering difference - 1997
  • Probablility distributions for estimating the |F|s - 1997
  • Computationally assisted - 1997
  • Texture-based method - 1997
  • Computer prediction - 1996
  • Simultaneous translation and rotation of a structural fragment within the unit cell - 1996
  • Combination of high-resolution X-ray powder diffraction and molecular modelling techniques - 1996
  • Generalized rigid-body Monte Carlo method - 1996
  • Solving crystal structures with the symmetry minimum function - 1995
  • Static-structure energy minimization method - 1995
  • Computer modelling approach - 1995
  • Tangent formula derived from Patterson-function arguments - 1995
  • Real-space scavenger - 1994
  • Bayesian approach - 1994
  • Optimal symbolic addition program - 1993
  • Entropy maximisation and likelihood ranking - 1991-1992
  • Monte Carlo - 1991
This impressive list shows the current interest in developing new methods in SDPD. The subject is really quite hot. It will not be possible to consider every method here, since few programs are available. But you should undoubtedly keep in mind their existence. At this stage, I would recommend you to get and read the raw litterature explaining more or less in details how these methods are working. Go to the Programs and Methods Web page, select a program name (GAP, ROTSEARCH, OCTOPUS...), use it as keyword into the search system, and you will get references for that program use on experimental cases (if any...). Read also some of the review papers (CD) listed in the SDPD-Database. Some of them review exclusively peculiar topics, like direct methods only, or Monte Carlo and simulated annealing only, or more generally, the molecule location methods. Other reviews are compound-type oriented.

Other recommended lectures :

Have a look at the EXPO CCP14 tutorial (CD) Web pages. EXPO integrates EXTRA, a program addressed to full pattern decomposition (Le Bail method) and SIRPOW-92, which applies direct methods for solving crystal structures. The package exploits supplementary amount of information which become available during the phasing process : 

    the preferred orientation, 
    the pseudo-translational symmetry, 
    the positivity of the electron density,
    the positivity of the Patterson function, 
    a well oriented and positioned fragment. 

Such an information allows theoretically to improve the pattern decomposition in EXPO (though evidences of such improvement were never clear to us, moreover, it should be noted that no independent study led to the same conclusion : only the promoters of the method declared improvement). This is why EXPO is included in the "special methods". Other program able to use similar informations are DOREES, FIPS (...) but those programs are not freely available, to our knowledge. Using them may lead you to start some collaboration with the authors.

See the Focus (R.W. Grosse-Kunstleve) documentation.

See Zefsa II (M. Falcioni and M.W. Deem). Read one of their paper in PDF (on the CD) format, and see the CCP14 Web pages (CD).

You may also download these two above programs. They are both devoted to solve framework structures (like zeolites). See also the Zeolite Group homepage, maybe there will be something new.

Read the ESPOIR manual (CD) about structure determination by Monte Carlo from Scratch, that is to say, from a random starting model (at this stage, exclude the molecule location or molecule replacement method part which is reserved for the next week). See a paper in PDF format (on the CD) in which ESPOIR is used in "scratch" mode.

Have a look at FOX and PSSP which are freely available, like ESPOIR.

Commercial programs doing some special things are :

Endeavour by H. Putz, J.C. Schoen, M. Jansen (CD : PDF paper)

TOPAS by Bruker

DASH by W.I.F David and K. Shankland

PowderSolve/Materials studio from Accelrys/MSI (CD : PDF paper)

Software to download

At that time, you should already have obtained EXPO. The cimetidine example distributed with the package is extremely easy to deal with : you just have to press the "continue" button up to the structure solution. Other programs to download are :

ESPOIR by A. Le Bail. Open source (CD - and  see the PDF file).

FOX by V. Favre-Nicolin (see also FOX at the CCP14 if some links do not work). (CD - and see the PDF file).

PSSP by P.W. Stephens (CD).

If you have ideas about other freeware, they are welcome. 

If you are a bit confused now, this is quite normal, you are at the frontier of high level research.


0- Forget what you do last week.

1- Apply EXPO to Na5Cr3F14. The .pow and .exp files are already prepared for a standard approach. Give your final best list of atomic coordinates together with the Reliability factors. Try to resist to using the final Rietveld facility inside EXPO.

Note that exercise 2 would be hard to realize exclusively with EXPO since the powder pattern shows a mixture of 2 compounds, and EXPO prefers single phase patterns.

2- Apply ESPOIR (or -if they can do that job - FOX, or PSSP or ?) to the compound synthesized in the system PbF2/CrF3/HFaq for locating the heavy atoms (Pb and Cr). It is suggested to use several hypotheses about the Pb/Cr ratio: 1:1 ; 2:1 and 1:2 (corresponding respectively to the PbCrF5, Pb2CrF7 and PbCr2F8 formulations (Z=4 for each case). The .dat and .hkl files for Pb:Cr = 1:1 are already prepared for using ESPOIR. According to the best result, try to find also the F atoms with ESPOIR (or Endeavour, if still available for free). Give your final best list of atomic coordinates together with the Reliability factors.

Software selected for the correction

EXPO for exercise 1. ESPOIR for exercise 2.

The next week will be reserved for Structure solution by Patterson, direct or molecule location methods, part 3.
Good luck !