Generating the Fragment Information

Use CORINA

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.

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Cartesian Co-ordinates Generated by CORINA

(Use a cell size of 0,0,0 to tell ESPOIR that you have input Cartesian Co-Ordinates)

  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

   23.0670   13.3440    7.0880    90.000    90.000    90.000
 0.614300    0.344100    0.140000  1.
 0.545800    0.457000    0.202000  1.
 0.556900    0.186000    0.185000  1.
 0.562200    0.296000    0.185000  1.
 0.519900    0.363000    0.218000  1.
 0.455800    0.359000    0.272000  1.
 0.603000    0.439000    0.158000  1.

• Armel Le Bail's ESPOIR Software - http://sdpd.univ-lemans.fr/sdpd/espoir/

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.

• Armel Le Bail's Overlap Software - http://fluo.univ-lemans.fr:8001/ftp/overlap.zip
  [US Mirror] | [CCP14 UK Mirror] | [CCP14 Canadian Mirror] | [CCP14 Australian Mirror]

Creating the ESPOIR Control file (filename.dat)

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.

• Remember: use the Fobs HKL data NOT the Fsquared HKL data!
  (have already made this mistake myself - Lachlan)

• (Note: using the Windows cut and paste can save a lot of problems, expecially minimising the introduction of typographical errors)

• (Note: If using the "regenerated pseudo-pattern", you will be prompted to give the U,V,W from the Le Bail fit. Please have this information handy. The following HKL file was Le Bail fitted using Fullprof)

• When prompted, give the filename (in this case cime)
• When prompted, give an identifier (in this case cime)
• Give the cell constants (you can use a Windows cut and paste - wiggle the mouse a bit if the pasting seems to pause. Such are the mysteries of MS-Windows.) (10.394251 18.819084 6.825021 90.000000 106.437195 90.000000)
• Give the spacegroup (P 21/A) Note that this is a non-standard setting and may give problems later when viewing in "Default" Platon - in putting the connectivity out of whack. Also, different programs may handle the default connectivity differently.
• Give the wavelength. (1.52904)
• This is X-ray data (the codeword is 4)
• There are 17 non-hydrogen atoms in this structure; thus enter 17
• There are 3 different atom types.
• There are two object (the rigid body and the freely moving atoms) - so enter 2
• When in doubt (especially if there is an overlap problem), fit on the regenerated pseudo-pattern: = 1
• Get the printouts.
• Give the U,V,W from the Le Bail fit. (0.00414 0.00042 0.00144)
• Give the number of points above for the pseudo powder pattern (I tend to say 4)
• When prompted, give the Atom Types one at a time. (S N C)
• We will not be providing bond contraints. (0 = no)
• Give maximum move (in Angstrom) for each atom type. Not sure of a good rule here - I guess you find out by trial and error(?), I just copied from the ESPOIR example site (7)
• Give the annealing law: go with the default: 2 (unless you have another option?)
• Give sigma : the data precision - go with the default: 1
• Give reject: I tend to go with 0.005 instead of the default of 0.001
• Give number of moves between prints (I tend to go for 5000)
• Give the maximum number of moves: Go with default of 200000
• Give the maximum number for saving: I tend to go with 20000
• If after nstart events, the R factor is larger than rmax, then restart Give nstart and rmax: (I tend to blindly go for the defaults: 40000 and 0.2) (so ESPOIR will reject any solution about 20% after 40,000 moves)
• I like to fit on "R", thus enter 2
• Go for the default number of Runs (10) - you may have to optimise this over time.
  • IMPORTANT: Depending on the size and nuances of the structure, the number of trials that it will take for ESPOIR to stumble on a solution could vary considerably. In the case of Cemitidine, it has been found that 1 out of 50 trials may succeed - but you only find this out the hard way. Thus take this into account in that if ESPOIR fails within a certain number of trials, you may have to increase the number of trials; or consider changing some of the options (and increasing the number of trials). Such is life with real-space structure solution methods.

  • Check the ESPOIR help area for advice in this regard: http://sdpd.univ-lemans.fr/sdpd/espoir/examples/index.html. Advice is available on the web about molecular organics include Cimetidine, Pyrene and 1-methylfluorene: http://sdpd.univ-lemans.fr/sdpd/espoir/examples/index.html#Cimetidine | http://sdpd.univ-lemans.fr/sdpd/espoir/examples/index.html#pyrene | http://sdpd.univ-lemans.fr/sdpd/espoir/examples/index.html#1-met

  ---

• For Object Number 1 (we will define this as the rigid body)

• We are using a rigid body, and NPERM of 10 seems nice thus enter 2 10

• When prompted for number of Sulphur atoms: 0
• When prompted for number of Nitrogen atoms: 2
• When prompted for number of Carbon atoms: 5
• Enter a thermal value - ESPOIR suggests 3 for Organic.
• Using occupancy of 1 for all atoms: Enter 0
• Try a guess that all atoms are on general positions: Enter 0

• For Object Number 2 (we will put the freely moving atoms in this Object)

• We are using randomly generated freely moving atoms atoms, and NPERM of 10 seems nice thus enter 1 10

• When prompted for number of Sulphur atoms: 1
• When prompted for number of Nitrogen atoms: 4
• When prompted for number of Carbon atoms: 5
• Enter a thermal value - ESPOIR suggests 3 for Organic.
• Using occupancy of 1 for all atoms: Enter 0
• Try a guess that all atoms are on general positions: Enter 0

• Enter any number (try 4?) to finish with PRESOIR

Following is the nearly completed ESPOIR file generated by PRESPOIR:

cime                                                                            
!    a,     b,     c,    alpha,    beta,    gamma
  10.3943  18.8191   6.8250    90.000   106.437    90.000
! space group
P 21/A                              
! lambda, radiation, N of atoms, types of atoms, N of objects, "|Fobs|" or patterns, iprint
1.52904   4  17   3   2   1   1
! U,     V,     W,    STEP
  0.00414  0.00042  0.00144   4.
! atom names, in 8A4
S   N   C   
! code for minimal distance contraints
 0
! maximum moves for each type of atom
   7.000   7.000   7.000
! annealing law, sigma, reject
  2.0000  1.0000  0.0010
! number of events for : print, maximum, save
      5000    200000     20000
! events for restart, rmax, ichi, number of runs
 40000  0.200   2  10
! object type and NPERM for object   1
   2  10
! number of atoms of each type in object   1
   0   2   5
! B overall, NOCC, NSPE for object   1
 3.0 0 0
! cell parameters, and x, y, z, occup. for object   1
Add there the cell parameters
  and the x,y,z, occup. for your object   1
! object type and NPERM for object   2
   1  10
! number of atoms of each type in object   2
   1   4   5
! B overall, NOCC, NSPE for object   2
 3.0 0 0

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.

cime                                                                            
!    a,     b,     c,    alpha,    beta,    gamma
  10.3943  18.8191   6.8250    90.000   106.437    90.000
! space group
P 21/A                              
! lambda, radiation, N of atoms, types of atoms, N of objects, "|Fobs|" or patterns, iprint
1.52904   4  17   3   2   1   1
! U,     V,     W,    STEP
  0.00414  0.00042  0.00144   4.
! atom names, in 8A4
S   N   C   
! code for minimal distance contraints
 0
! maximum moves for each type of atom
   7.000   7.000   7.000
! annealing law, sigma, reject
  2.0000  1.0000  0.0010
! number of events for : print, maximum, save
      5000    200000     20000
! events for restart, rmax, ichi, number of runs
 40000  0.200   2  10
! object type and NPERM for object   1
   2  10
! number of atoms of each type in object   1
   0   2   5
! B overall, NOCC, NSPE for object   1
 3.0 0 0
! cell parameters, and x, y, z, occup. for object   1
   23.0670   13.3440    7.0880    90.000    90.000    90.000
 0.614300    0.344100    0.140000  1.
 0.545800    0.457000    0.202000  1.
 0.556900    0.186000    0.185000  1.
 0.562200    0.296000    0.185000  1.
 0.519900    0.363000    0.218000  1.
 0.455800    0.359000    0.272000  1.
 0.603000    0.439000    0.158000  1.
! object type and NPERM for object   2
   1  10
! number of atoms of each type in object   2
   1   4   5
! B overall, NOCC, NSPE for object   2
 3.0 0 0

Running ESPOIR

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