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:
IntroductionOnce 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. This tutorial will go through a few tricks with generating "realistic" fragments (given we already know the answer to this problem).
Generating the Fragment Information(this is cut and pasted into the file generated by prespoir later)
You can use a vareity of techniques to generate a fragment. You can either give ESPOIR a fragment in "cartesian" co-ordinates, or give it the fragment from a determined structure in crystallographic co-ordinates: [CORINA and Cambridge Database Searching Example] | [Generating a fragment in CORINA]
Be wary to use the area of the structure that you have good confidence is rigid. In the case of Cimetidine, you may not be sure where the Sulphur is located relative to the ring. This should be evident by looking at related structures within Platon.
Cartesian Co-ordinates Generated by CORINA
(Use a cell size of 0,0,0 to tell ESPOIR that you have input Cartesian Co-Ordinates)(If ESPOIR is told we have 2 nitrogens and 5 Carbons in the structure, the first two atoms on the following fragment list are Nitrogen, the next 5 carbon. This was using the smile string from the Java JME Molecular Editor: Cc1nc[nH]c1C and passing this to CORINA)
0.00 0.00 0.00 90.0 90.0 90.0 -1.087 -0.991 0.003 1. -0.919 1.160 -0.002 1. 1.600 1.476 0.001 1. 0.328 0.667 0.001 1. -1.772 0.172 -0.001 1. 0.245 -0.677 -0.002 1. 1.398 -1.648 -0.001 1.
Co-ordinates obtained from the Cambridge database
(Obtain the cell and structure, trimming it down such that you only have the fragment atoms of interest)
You can trim down the structure in a variety of programs, including the SXGRAPH program in WinGX
(Select atoms to trim)
(Save fragment in Shelx format)
(Cambridge Crystallographic atom positions of the rigid fragment in Shelx format)
TITL Ref. Number: 325 Ref. Code: ACMPIM10 Space Group: Pbca CELL 0.71069 23.0670 13.3440 7.0880 90.000 90.000 90.000 ZERR 1.00 0.0000 0.0000 0.0000 0.000 0.000 0.000 LATT 1 SYMM 1/2 + X, 1/2 - Y, - Z SYMM X, 1/2 - Y, 1/2 + Z SYMM 1/2 + X, Y, 1/2 - Z SFAC N O C H UNIT 16 8 96 96 MERG 2 WGHT 0.10000 FVAR 1.00000 N1 1 0.614300 0.344100 0.140000 11.00000 0.05000 N2 1 0.545800 0.457000 0.202000 11.00000 0.05000 C2 3 0.556900 0.186000 0.185000 11.00000 0.05000 C3 3 0.562200 0.296000 0.185000 11.00000 0.05000 C4 3 0.519900 0.363000 0.218000 11.00000 0.05000 C5 3 0.455800 0.359000 0.272000 11.00000 0.05000 C6 3 0.603000 0.439000 0.158000 11.00000 0.05000 HKLF 3 END
ESPOIR Friendly Format ready for cut and pasting into the ESPOIR *.DAT file generated by PRESPOIR
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 nearly completed ESPOIR file generated by PRESPOIR:
Now cut and paste the fragment information over the text Add there the....for your object 1 to give the ready to use ESPOIR DAT file.
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