SHELXTL and PLATON The computer programs at the heart of the Purdue package.
Working with UNIX files • File names are case sensitive. • UNIX does not recognize file types (.xxx) but many programs do • Remove a file—rm file • Copy a file—cp oldfile newfile • Rename or move a file—mv oldfile newfile
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
To get a brief list of the files in a directory the command is ls • For more complete information use ls –l • Wild cards—ls a* lists all files that begin with a.
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
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.
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 • Fhkl=Sfjexp(2pi(hxj+kyj+lzj) • Must adjust f for atomic motion
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(a+b+c)=ft(a)+ft(b)+ft(c)
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.
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.
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)
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.
What to Do. • Solve the structure. • Run non-linear least squares to adjust the positions, and adp’s of each atom and also an overall scale factor • Apply the phases from the Fcalc in step 2 to Fobs • Calculate a Fourier map and find new atom positions • Go to step 2. • Step 2-5 are called refinement
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
SHELXTL at Purdue • XPREP—a data analysis program that sets up the files for Shelxtl • XS—the SHELXTL direct methods program (public domain) • XL—the SHELXTL least squares refinement and analysis program (pd) • XH—a big version of XL (pd) • XP—the graphics part of SHELXTL also contains some utilities.
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.***
Files for XPREP • All programs assume the data is in a file named **.hkl (xl.hkl) • XPREP—input **.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.
Files for XS • Data file **.hkl • Input file **.ins from XPREP • Output file **.res—this has the same format as an .ins file but with the results of the program • Listing file **.lst • Run by issuing “xs xl”
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.
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
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!