SYSTEM-S

PLATON HOMEPAGE

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

• SYSTEM-S (or S for short) is a closely SHELX(S/L) compatible atomic resolution single crystal structure determination suite providing a unique crystallography aware SHELL functionality for the invocation and management of the 'tools-for-the-job'.

• SYSTEM-S is for the professional chemical crystallographer who is bored by the routine input/output preparation/analysis cycle, but knowledgeable about the procedural details and aware of all signals of possible trouble.

• SYSTEM-S operates as a supervisor (with a crystallographic degree and with an organized memory) over the process of a single crystal structure determination by X-ray diffraction techniques.

• SYSTEM-S provides an interface to a variety of established datareduction, structure determination, refinement and evaluation tools.

• SYSTEM-S provides an environment in which it is made easy to tackle 'hard'-structures requiring multiple attempts to solve a structure in different space groups and with different structure solution methods.

• SYSTEM-S provides two modes of operation:
  1. Guided Mode: The program suggests the course of the structure determination on the basis of the current context.

  2. Automatic Mode: An automatic structure determination from primary data to final (refined) results is attempted. This mode will be referred to as the No-Questions-Asked (or NQA) mode.

  The NQA-mode obviously works only in the case of (relatively) trouble free structures (i.e. no disorder, twinning and similar specialist issues).

• The tools available within SYSTEM S are either build-in (i.e. part of PLATON) or external (i.e. plug-ins).

  External:

  • SHELXS97 - http://shelx.uni-ac.gwdg.de/SHELX/
  • SHELXL97 - http://shelx.uni-ac.gwdg.de/SHELX/
  • SIR97 - http://www.ba.cnr.it/IRMEC/SirWare.html
  • DIRDIF99 - http://www-sci.sci.kun.nl/xtal/dirdif/
  • CRUNCH-1.1 -http://chemb0b.leidenuniv.nl:80/~rag/

  Note: CRUNCH should run in the foreground (as opposed to the default:background)
  (This should be changed in crunch.uni, line 490)

  Build-in:

  • PLATON - Geometry Calculations etc.
  • ORTEP - Stripped ORTEP
  • SHXT86 - Stripped, Adapted & Modified old but powerful SHELXS86/TREF.
  • PLUTON - Molecular Graphics
  • HELENA - CAD4-datareduction
  • EXOR - Work-up/completion of raw E-map's
  • ABSTOMPA - Exact correction for absorption
  • DELABS - Empirical correction for absorption

• Both SYSTEM-S commands such as SHELXL ISO 3 (for three cycles of isotropic least squares refinement with the program SHELXL97) and standard UNIX-SHELL commands such as ps -aux (to see what is going on) can be given on the S-SHELL prompt.

• SYSTEM-S sets up a directory tree for the storage of information supplied and generated during the structure determination and manages input/output for the available set of crystallographic tools.

• SYSTEM-S restarts, when re-invoked with a compound name in the context where it was terminated during the last invocation. The current context can be reset to an earlier context with the RELINK, TRMX and SPGR commands.

• SYSTEM-S is the default tool used and developed in the context of our National Service Crystallography Center (Utrecht, The Netherlands) handling over 200 (mainly organometallic) structures per year and building on experience gained from over 2000 structure determinations.

• SYSTEM-S comes as a build-in feature of PLATON.

• SYSTEM-S is (currently) available only on the UNIX/LINUX Platform due to extensive use of typical UNIX-SHELL features (e.g. sort, ln).

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

• s is in the PATH (e.g. with the soft link to the platon executable i.e. 'ln -s platon s')

• shelxs and shelxl are in the PATH (or set with the environment variables SHSEXE and SHLEXE respectively).

• The two files sdemo.ins and sdemo.hkl are available in the current working directory from which S will be invoked.

TITL SDEMO
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
HKLF 4

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.

Remarks:

• 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.

4 - Worked Example in the Guided Mode

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 CRUNCH 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:
s[SHELXL ISO].

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.

6 - PRIMARY (RAW) DATA

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