The platon crystallographic package - səhifə 67
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Example for setting PLAEXE in the (t)csh-shell:
setenv PLAEXE /mnt/spea/bin/platon
when the platon executable is in /mnt/spea/bin
10.3 - DEMO run(s) of S for C(10)H(12)O(6)
- sis in the PATH (e.g. with the soft link to the platon executable i.e. 'ln -s platon s')
shelxlare in the PATH (or set with the environment variables SHSEXE and
- The two files
are available in the current working directory
from which S will be invoked.
sdemo.inscontains relevant information for a small organic compound (with formula
C10H12O6), on the cell, the wavelength ,info on the expected cell-content and HKLF 3 or 4
type, all in SHELX-style.
CELL 0.71073 4.0007 7.7300 16.7597 90.0540 94.0760 90.0528
ZERR 2 0.0010 0.0008 0.0022 0.0096 0.0160 0.0144
SFAC C H O
UNIT 10 12 6
Note: no spacegroup information required. Data/instruction lines other than the above are
ignored. The CELL should be consistent with that of the reflection file.
sdemo.hklcontains a standard shelx HKLF 4 style dataset
S can now be run in the auto-mode (the
No-Questions-Askedmode) with the keyboard
s sdemo.ins nqa
After some time (during which the space group is determined, the structure is solved by
direct methods (SHELXS) and refined (SHELXL) including H-atoms) the result of the
analysis is shown as a rotating molecule.
The rotation can be stopped by clicking in the window.
S can be terminated by typing 'END'.
Alternatively, S can be started in the 'guided' mode via:
An interactive sequence is set up in response.
User input routinely involves 'hitting-the-return-key' when the suggested material within 
is o.k (or clicking on ACCEPT-DEFAULT in the menu bar).
An 'END' instruction terminates S.
S will return to the status where it was when restarted.
- 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
- 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
- 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
10.4 - Worked Example in the Guided Mode
Start the structure determination with
The s-shell prompt should look like
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.
The next suggested logical step, i.e
is the determination of the lattice type
and Laue group with associated transformation matrix. Hitting the return will bring up a
number of options.
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.
The next step
s[SPGR]brings up the section of the space group specification. A number of
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.
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.
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.
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).
Indeed, all noise peaks have been removed and element types correctly assigned as shown in
If not, as may be the case with more problematic structures, PLUTON may be used
to RENAME atoms to their desired labels and atom types for those mis-assigned by the
automatic procedure. Also, remaining ghosts may be removed from the current model
(stored in s.res; and optionally to be inspected by clicking on the LstRES Menu-button) with
On the termination of PLUTON, S suggests isotropic refinement as the next step:
At the end of the refinement a difference map is calculated from which the highest peaks
can be appended to the parameter file to be inspected with PLUTON. In the current case, no
significant residual density is found. Hit RETURN.
This step is followed by anisotropic refinement indicated with
In the next step it is suggested to find H-atom positions in a difference fourier map which is
effected by hitting the RETURN key on
s[HATOMS]. The result is again shown in a
The atom list may be edited in this stage.
Intermediate SHELXL refinement results and warning display look like
In the next step, H-atoms are included in the refinement.
The final step involves a weighted refinement.
This step can be repeated until
Terminate with END.
The results of the current refinement are in ~USER/s/sdemo/tm/sg/shelxl.
10.5 - DIRECTORY STRUCTURE of SYSTEM S
S operates in a directory structure under 'CURRENT_DIR/s/' (or '~USER/s/').
Note: '~USER/s/' is always used once this directory exists (either deliberative or as a result
of a user error)
Each project (structure) has its own subdirectory tree starting with the name of the structure
(e.g. sdemo). The top-level directory for a structure is indicated as 'level-0'
Sub-directories of a level-0 directory include level-1 trees (one for each lattice type that is
Sub-directories of a level-1 directory include level-2 trees (one for each space group
attempted to solve the structure in).
Level-2 houses subdirectories for the varies structure determination and refinement tools
and there associated data.
The TREE instruction provides a display of the tree structure.
(Note: TREE does not display hidden files (stating with .) that should not be touched, since
they perform 'memory'-functions)
The complete directory tree for a given compound
compoundcan be removed either from
buttons on the SYSTEM-S menu or via the command line instruction:
s compound remove
0.6 - PRIMARY (RAW) DATA
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