SHELXTL and PLATON

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SHELXTL and PLATON

• The computer programs at the heart of the Purdue
  package.

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Working with UNIX files

• File names are case sensitive.
• UNIX does not recognize file types (.xxx) but
  many programs do
• Remove a filerm file
• Copy a filecp oldfile newfile
• Rename or move a filemv oldfile newfile

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Working with Unix Directories

• Every file is in a directory (the prompt)
• Directories may contain sub directories
• .. Is the directory above
• . Is the current directory
• To change directory cd
• If cd /abc goes to direcotry abc while cd abc
  goes to subdirectory abc in current directory

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• To get a brief list of the files in a directory
  the command is ls
• For more complete information use ls l
• Wild cardsls a lists all files that begin with
  a.

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Useful Linux Tricks

• You can re-enter a previous command by using the
  up arrow to find it
• Entering a tab will try and complete a partial
  file name
• You can highlight text by dragging the mouse over
  it while holding down the right button
• You can copy highlighted text by pressing the
  middle button

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Where do we go.

• Ideally all that is needed is to run a Fourier
  transform on the data to obtain an electron
  density map.
• However as was shown earlier, the positions are
  contained in the phases.
• There is no phase information in our data.

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Some Ideas

• The electron density in the crystal is the sum of
  the individual electron densities of the atoms
  each placed in its proper position. This ignores
  bonding
• Likewise, in reciprocal space the scattered
  intensity is the sum of the scattering factor of
  each atom in its proper place
• FhklSfjexp(2pi(hxjkyjlzj)
• Must adjust f for atomic motion

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• The Fourier transform of a sum is equal to the
  sum of the Fourier transforms of the components
• Let ft mean Fourier transform
• Then ft(abc)ft(a)ft(b)ft(c)

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Fcalc

• Since we can use the summation of the scattering
  factors to generate F this is called Fcalc
• Note the Fcalc contains not only the amplitude of
  F but also the phase.
• We can get phase information by placing some
  atoms in the correct positions, calculating F and
  the applying those phases to Fobs.

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Solving the Structure

• Before we can proceed, a minimum of 15 of the
  electron density must be placed correctly in the
  cell.
• Of course the location of the electron density
  (atoms) is what is to be determined and is
  usually unknown.
• Bootstrapping a start is referred to as solving
  the structure.

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Methods of Solution

• If you have a few atoms which have higher atomic
  numbers than the majority of atoms then locating
  just these atoms may give good enough phases to
  get started. This is referred to as heavy atom
  methods.
• This is usually done through the Patterson map
  which can be solved manually of automatically
  (dirdif patty)

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• A second approach is to try to find the phases
  directly. This is called direct methods.
• Typically direct methods works best when all the
  atoms have about the same atomic number
• When it works it tends to find all the atoms.

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What to Do.

1. Solve the structure.
2. Run non-linear least squares to adjust the
   positions, and adps of each atom and also an
   overall scale factor
3. Apply the phases from the Fcalc in step 2 to Fobs
4. Calculate a Fourier map and find new atom
   positions
5. Go to step 2.
6. Step 2-5 are called refinement

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SHELXTL

• SHELXTL is a commercial () refinement package
  sold by Bruker-AXS.
• It consists of several programs we will use and
  some we will not.
• The package is programmed by Dr. George Sheldrick
  at the University of Gottingen in Germany
• George is a superb programmer

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SHELXTL at Purdue

• XPREPa data analysis program that sets up the
  files for Shelxtl
• XSthe SHELXTL direct methods program (public
  domain)
• XLthe SHELXTL least squares refinement and
  analysis program (pd)
• XHa big version of XL (pd)
• XPthe graphics part of SHELXTL also contains
  some utilities.

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Using SHELXTL

• Each program is called from the command line by
  entering its name (i.e. xl or xh)
• A second input is the problem name. To use files
  named abc. enter xl abc
• If no problem name is entered it defaults to the
  program name. For example xl is the same as xl
  xl.
• At Purdue we will assign all the files xl.

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Files for XPREP

• All programs assume the data is in a file named
  .hkl (xl.hkl)
• XPREPinput .p4p (xl.p4p)output .ins
  (xl.ins)
• The p4p file can be created using the program
  p4p.
• The xl.ins file is copied into a file xl.org
  which is saved throughout the refinement.

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Files for XS

• Data file .hkl
• Input file .ins from XPREP
• Output file .resthis has the same format as an
  .ins file but with the results of the program
• Listing file .lst
• Run by issuing xs xl

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Files for XL and XH

• Data from .hkl
• Input from .ins
• Output to .lis
• Next input file to .res
• xl or xh xl
• Before rerunning xl must rename .res to .ins
  or will rerun the same data.

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PLATON

• This is a crystallographic tool box which
  contains many useful functions
• It is written by Anthony (Ton) Spek at the
  University of Utrecht in the Netherlands.
• It is a huge program containing over 140,000
  lines of Fortran code
• It is free to academic users.
• There is a Windows version

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Input to PLATON

• PLATON has very flexible input.
• It can read SHELX data using .res or .ins as
  input and .hkl as data. (platon xl.res)
• It can read cif files.
• It outputs a ton of files!