- All calculations are done in a subdirectory of the directory 's'.
Directory 's' will be created automatically in the current directory unless there exists
already such a directory in '~USER'.
- Calculations on the sdemo example may be restarted in the context where it was left
with
's sdemo'.
- To remove the 'sdemo-stuff' from this tree goto directory 's' and do a
'
rm -r sdemo'
- PLEASE NOTE: S is not finished, there are several loose ends where more work has
to be done or in progress (non-standard refinement, absorption correction other than
DELABS etc).
- Final refinement can be taken up with the files in 's/COMPOUND/tm/sg/shelxl'.
A second example (C13 H24 N2 Pd), illustrating a structure determined automatically by
heavy atom methods (DIRDIF99), can be run with
sdemo1.ins
and
sdemo1.hkl
.
10.4 - Worked Example in the Guided Mode
Start the structure determination with
s sdemo.ins
The s-shell prompt should look like
s[CELL]
(Fig.1)
Hitting the return key (or clicking on ACCEPT-DEF) will bring up the section of S that
establishes the cell dimensions and associated esd's. In the current case we just acknowledge
(with a return) the correctness of the values found in sdemo.ins. When desired, cell data
may be changed at this point.
(Fig.1a)
The next suggested logical step, i.e
s[TRMX],
(Fig.2)
is the determination of the lattice type
and Laue group with associated transformation matrix. Hitting the return will bring up a
number of options.
(Fig.3)
The suggested choice (#1) is accepted again with a RETURN.
The second option (#2) could be attempted lateron when #1 doesn't lead to results.
(Fig.3a)
The next step
s[SPGR] brings up the section of the space group specification. A number of
choises,
(Fig.4)
based on the observed systematic extinctions, is suggested, along with an a-
priori choise (#14).
The next step
s[FORMULA] brings up the section to specify the cell content. In our case,
the formula given in sdemo.ins is suggested.
(Fig.5)
However any other specification is
possible. Here we accept the suggestion.
This brings up
[Z]. Hitting RETURN will generate a suggested value for Z (i.e. 2). Any
other reasonable value may be entered here. In our case we just hit RETURN again.
This brings us to the core of a structure determination, i.e. the phase determination. S
suggests to run SHELXS for this.
(Fig.6)
Alternatively, the older SHELXS86 (as opposed to
SHELXS97), SIR or SIR2004 could be attempted when available on the machine. Here we
again take the default choice.
The result of the SHELXS/TREF calculation is now shown for inspection with PLUTON.
(Fig.7)
PLUTON can be terminated by clicking on EXIT.
The list of atoms generated with SHELXS obviously needs some 'cleanup'. This can be done
with a procedure called EXOR (short for exorcise).