This example uses example Cimetidine data from the EXPO 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:
Once Direct Methods and Patterson methods are exhausted, a method of last resort
is to use real-space techniques such as the Monte Carlo method offered in
Armel Le Bail's ESPOIR software (as of writing, version 3 was just released). This can
take hours (more likely days, possibly weeks, maybe months) to
run and there is no guarantee it will solve as per the random
combinations tried by the ESPOIR software. A way to make it more likely to solve is
to introduce rigid fragments if this is possible (which is part of another ESPOIR
tutorial). This tutorial will go through the basic setup that might work: in all the atoms
freely moving with no bond restraints or fragments.
Obtain the F's (NOT Fsqures) HKL file from the Le Bail fit (you can use the extra.hkl file generated by EXPO if you ran this already). Use Armel Le Bail's overlap software to process and convert the HKL file into Shelx F's format (filenameF.hkl is the output file) using the "0" option so as not to lose any reflections.
As ESPOIR can reconstruct the profile from the HKL file (which is the method we will use here), you MUST tell the OVERLAP HKL processing software to keep all the reflections by using "0" to signify that all reflections are to be kept irrespective of the degree of overlap. If you do not do this, the reconstructed profile will not be correct as it will be missing intensity from the overlapped reflections.
Generally (advice from Armel) you want 10 observations (HKLs) per atom. So if you have 17 non-Hydrogen atoms to find, 200 reflections could be OK. You can use more, but this will increase computation time. Using a fragment can save on computation time instead of using freely moving atoms - providing there is a rigid fragment that can be defined. 50 HKLs per multi-atom fragment is recommended by Armel.
Creating the ESPOIR Control file (filename.dat)Before running ESPOIR, the Espoir control file has to be created. It is possible to reuse a file but you may miss-interpret the meaning of a parameter causing unexpected results. Initially it would be better to generate the file from scratch using the PRESPOIR program.
ESPOIR and PRESPOIR use a DOS like interface so you would normally run it from the command line (go into the subdirectory where the files are located and call the programs the old fashioned way)
ESPOIR is developing all the time so it is good to check for updates. Tonight's update (17th April 2000) is that ESPOIR has Fullprof like comments in the control file (filename.dat) - hurrah! You may have to fiddle around to get ESPOIR working to your satisfaction in solving structures successfully.
To make a start, open up a DOS Command prompt and enter the directory with the data. Type prespoir to be given the following window.
Following is the completed ESPOIR file generated by PRESPOIR:
Type espoir and when prompted for the control file, enter cime (or whatever the filename is - no file extension) .
Observing the Results
Espoir will generate a "backup" Platon SPF file and shelx INS file each specified number of cycles that you requested in the control file. Use Platon or Ortep-3 (or you favourite structure viewing software) to view the file.
Warning: As stated above, one problem when using a non-standard spacegroup and Platon is that it may convert into a standard setting that could affect the of the structure. Though each program may have different "default" views of the structure and may require some tweaking. (for instance: in Ortep-3 - growing the fragments.
Platon View - converted into a standard setting
Ortep-3 view - may have to grow fragments/expand the cell
SXGRAPH - soon to be released in the next WinGX - allows Assembly of residues and Growing Fragments