About the tutorial
This tutorial is intended to explain the common steps of the structure solution and refinement of a 'small molecule' with less than 100 non-hydrogen atoms, using the SHEXTL program suite.
|Optionally all steps explained within these pages for the structure example can be performed in practice by the user. Therefore you have to change to directory tutorial/user (look in the Linux basics if needed) and follow the green instructions in the bright blue coloured boxes (like this one).|
|All text chapters for steps 1-5 of the
tutorial have been designed as follows: Paragraphs refering to user
action (commands etc.) have a bright blue background. Other text explains
the figures as well as important crystallographic concepts. Additional information
and background knowledge has been left out on purpose. If you are
further interested in crystallography you should consult the links
to the glossary where many keywords are explained (still on beginners'
Should you get stuck on a certain stage of the project, look at the files in directory tutorial/save, where the (preliminary and final) results of each chapter are stored. If all works well, your files in tutorial/user should look the same in the end.
The examplary structure
3D model has been created with the final atomic coordinates of the structure
determination; thus it already shows the result of the tutorial steps.
Of course, real life is more exciting, as the structure may turn out to be
Programs and files
scheme shown here is an overview illustrating the sequence of programs
and the information flow (i.e. file transfer) between the programs.
The tutorial starts at a stage where the
x-ray diffraction experiment on the crystal has been finished and all reflection
data has been collected. Data processing - integration,
and some other corrections - have also
been made already. The structure determination so far resulted in a non-merged
HKL file, called momo-new-unmerged.hkl
in our case. (see step 2 - XPREP tutorial). Besides the cell parameters
(and knowlegde about the expected molecule) you only have that file at
the beginning of the tutorial. With the help of XPREP, the data
set has to be merged after having confirmed/determined the cell geometry
and space group. The merging reduces the number of data while enhancing
the quality. During the following structure determination steps the merged
HKL file momo-new.hkl will not be further
modified. It will always be needed by the respective programs for structure
solution and refinement.
Hopefully, this short introduction has given you a first outlook on the tutorial. Next comes the first tutorial step explaining the use of XPREP. If you are not familiar with Linux, the crash course included in these pages is strongly recommended.