Look here for an alternative System-S tutorial by Lachlan Cranswick (CCP14).



  1. What is 'SYSTEM-S'

  2. Implementation Requirements

  3. DEMO run(s) of S for C(10)H(12)O(6)

  4. Worked Example in the Guided Mode

  5. Directory Structure of SYSTEM S

  6. Primary (Raw) Data

  7. Other Try-it-Yourself Examples

  8. How to Implement the new Space group suggested by ADDSYM

  9. How to run S on a 'CIF/FCF' Dataset

  10. KappaCCD/Denzo to PLATON/S interface

  11. Summary of S-Instructions



The external tools (SHELXS97, SHELXL97, SHELXD, DIRDIF99, SIR97, SIR2002) are used 'as supplied' by their respective authors and should be obtained from the sources given below. They are NOT provided as part of this distribution. S will NOT work when no SHELX-97 executables are found in the PATH.



It is assumed by default that all programs called from PLATON/S are in the path so that PLATON/S can find them.

If not, environment parameters should be set:

Example for setting PLAEXE in the (t)csh-shell:

setenv PLAEXE /mnt/spea/bin/platon

when the platon executable is in /mnt/spea/bin

3 - DEMO run(s) of S for C(10)H(12)O(6)

Assumptions: sdemo.ins contains 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
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.hkl contains a standard shelx HKLF 4 style dataset

S can now be run in the auto-mode (the No-Questions-Asked mode) with the keyboard instruction:

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:

s sdemo.ins

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.


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.

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 choise (#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 SIR2002 could be attempted when available on the machine. Here we again take the default choise.

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).

Indeed, all noise peaks have been removed and element types correctly assigned as shown in (Fig.8) 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 PLUTON.

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 s[SHELXL ANISO].

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 PLUTON plot. (Fig.9) The atom list may be edited in this stage.

Intermediate SHELXL refinement results and warning display look like (Fig.9a)

In the next step, H-atoms are included in the refinement.

The final step involves a weighted refinement. (Fig.10) This step can be repeated until complete convergence.

Terminate with END.

The results of the current refinement are in ~USER/s/sdemo/tm/sg/shelxl.


S operates in a directory structure under 'CURRENT_DIR/s/' (or '~USER/s/').
Note: '~USER/s/' is always used once this directory exists (either deliberatery 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 attempted).

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 compound can be removed either from buttons on the SYSTEM-S menu or via the command line instruction:

s compound remove


S provides three options for the storage of the original (raw) diffractometer data from which S can be started.

  1. With COMPOUND.ins and COMPOUND.hkl (or COMPOUND.fcf) data in the current directory

    Example: s sdemo.ins

  2. With the raw shelx reflection data stored in a directory below the default (i.e. /mnt/shxdata) location.

    E.g. Shelx data (i.e. shelx.hkl and shelx.ins) for compound s1000 are stored in /mnt/shxdata/s1000

    S will find the data (shelx.ins & shelx.hkl) when started up with s s1000

    The default location can be changed by setting the environment variable SHXPATH to the proper alternative.

  3. In our local operation, CAD4 files (e.g. s1000.cad) are stored in a single directory /mnt/cad4data (i.e. /mnt/cad4data/s1000.cad).

    System S is started in this context as s s1000

    An alternative is to create an 's1000' sub-directory under 's' and copy the CAD4 data as s1000.cad into '~s/s1000'.

    System S is started as s s1000.


Following are adapted (i.e. no prior space-group information given ins the '.ins' data-file)
datasets supplied with Dr A.D. Hunter's SHELXTL course.

Example1: sfun1.ins and sfun1.hkl

Example2: sfun2.ins and sfun2.hkl

Example3: sfun3.ins and sfun3.hkl

Example of an inorganic compound Cs2TiSi6O15: csti.ins and csti.hkl

8 - How to Implement the new Space group suggested by ADDSYM

ADDSYM (either run explicitly or implicitly) will suggest an alternative spacegroup in RED on the main S window. Addsym is invoked automatically (unless switched off) at the start of the anisotropic refinement.

The transfer of the current structural results to the suggested space group is effected by clicking on 'TRMX' and 'SPGR'.

The Formula and Z can be adapted when desired following this transfer.

Refinement can now proceed in the new spacegroup.

Example: Solve the 'sdemo' structure not in P21/c but in Pc (# 7). At the anisotropic refinement stage, a message 'M/P P21/c' in RED will appear to attract attention to the possibly missed or pseudo-symmetry.

9 - How to run S on a 'CIF/FCF' Dataset

System S can be invoked using a 'fcf' (and 'cif') formatted file(s) (e.g. taken from the IUCR-Acta Cryst C Web-page) via:

s demo.fcf

S will convert the data in the .fcf file into a shelx.hkl (HKLF 4 format) file and ask for additional missing data.

The .hkl file can be found in the subdirectory 'hklf'.

A shelx.ins file is prepared from the data available in the 'fcf' file. Since an 'fcf' file doesn't contain information on the composition composition, this info should be given manually.

Alternatively, when both a 'CIF' and an 'FCF' (either with extension '.hkl' or '.fcf' is available, S can we invoked with:

s demo.cif

10 - KappaCCD/Denzo to PLATON/SYSTEM-S interface

The KappaCCD/Denzo software provides two output file formats

  1. compound.hkl - i.e. SHELXL structured file. In order to run SYSTEM-S, an additional compound.ins has to be prepared.

  2. import.cif - i.e. a reflection CIF containing both reflection data, cell dimensions, wavelength and optionally the supposed composition formula.

    SYSTEM-S can be started for this dataset via platon -s import.cif.


Warning: Not all options available yet in this version !!!


Absorption correction using a Gaussian Integration Grid.


Absorption correction following the de Meulenaer & Tompa analytical correction technique.


Extensive listing and display of the averaging and completeness of the reflection data as supplied.

The VIEW keyword invokes a display function giving a detailed view on the reciprocal lattice (completeness etc.)


Synonymous for the No-Questions-Asked mode.


Empirical absorption correction following the modified DIFABS (Walker & Stuart) approach.

DELABS is suggested by S in the isotropic refinement stage (and can be ignored when desired by asking for 'SHELXL ISO' as the next calculation.

DELABS can be repeated in any subsequent refinement stage. It always starts from the primary reflection file as supplied (with direction cosines). Anisotropic thermal parameters are automatically converted into corresponding isotropic U(eq) values before the DIFABS calculation.

It is a good idea to repeat the DELABS procedure when all scattering power is accounted for (including H-atoms).


The method of choise for heavy atom structures.

DIRDIF may have problems with structure determinations run with an incorrect CONTENTS formula, in particular when the number of heavy atoms is different from the number suggested.


Work-up of the 'raw' peaklist of a structure determination package (e.g. SHELXS).

Atom types are assigned to the resulting peaklist on the basis of the contents formula.

The correct identification of a peak as C,O or N may be hampered by difference in thermal parameters (i.e. periferal O atoms may fit the peak height of a carbon atom and a central C may fit the peak height of an O atom.


In function similar to EXOR but based on different techniques and using parts of SIR for it.


Face as part of the description of the crystal for face-indexed absorption correction.


Specification of the formula (e.g. C10H12O6).

In case no a-priori information is available, C1H2 may be used as a preliminary guess.


Find H-atoms in difference map.


Change absolute structure.


Local data-reduction program for CAD4-data.


Refresh parameter status listing.


This option provides a log of the previous calculations done for this compound.

It provides information to be used for RELINK.


In of Mu value (mm-1) for absorption correction.


This is the No-Questions-Asked mode to operate S. This option may be used to see whether a default structure determination leads to interpretable results. If not, various other options should be tried including solution in alternative spacegroups with alternative structure solution techniques.


Molecular geometry and other tools.


Molecular Graphics. Also used for the display of (intermediate) results, atom renaming and the introduction of HFIX-ed atoms.


Go to earlier context. See log-file.


Least-squares refinement on F^2.

Current options are: ISO, ANISO, HATOMS, WEIGHTS and the number of refinement cycles (default = 5 cycles).

Example: SHELXL ISO 3

Alternatively, SHELXL ISO 0 will provide a difference map that can be used in the cycle of model completion as an alternative for EXOR and EXORS.


Alternative for the lastest SHELXS (SHELXS86 occasionally solves structures that turn out to be more difficult with the latest version).


Default (Current version SHELXS-97-2) (I.e. fast) choice for the phase determination of light atom structures


SIR97 provides an excellent alternative for SHELXS. It is slower but often gives results with large poorly reflecting (low resolution) data sets.


By default, a list of spacegroups consistent with the current lattice, Laue symmetry and systematic extinctions is presented with an indication of a plausible first choice.


Transformation matrix (direct axes) for the transformation of the supplied reflection data to the desired lattice. By default, a selection may be done from a list of possibilities.


Z times FORMULA should specify the unit cell content. Z is not necessarily equal to the number of symmetry operations. It can be more or less.

The Default (Return) will suggest a suitable value (to be confirmed or overruled) giving reasonable density and volume-per-atom values.

06-Sep-2004 A.L.Spek