SYSTEM-S_*****_S-USERS_SHOULD_BE_REGISTRATED_SHELX-USERS_!_*****_The_external_tools_(SHELXS97,_SHELXL97,_SHELXD,_DIRDIF99,_SIR97,_SIR2002)'>Chapter 10 - SYSTEM-S
***** S-USERS SHOULD BE REGISTRATED SHELX-USERS ! *****
The external tools (SHELXS97, SHELXL97, SHELXD, DIRDIF99, SIR97, SIR2002)
are used 'as supplied' by their respective authors and may 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.
Development of SYSTEM S started around 1990 and aimed at the automation of data
reduction, structure determination, refinement and analysis of the results for data collected
with a serial detector based Nonius CAD4 diffractometer.
10.1 - WHAT IS 'SYSTEM-S'
- 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 three 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.
3. Silent Mode: Automatic 'filter' mode run from the command line.
The NQA-mode (and Silent 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:
4.
SHELXS97
- http://shelx.uni-ac.gwdg.de/SHELX/
5.
SHELXL97
- http://shelx.uni-ac.gwdg.de/SHELX/
6.
SHELXD
- http://shelx.uni-ac.gwdg.de/SHELX/
7.
SIR97
- http://www.ba.cnr.it/IRMEC/SirWare.html
8.
SIR200
4
- http://www.ba.cnr.it/IRMEC/SirWare.html
9.
DIRDIF
08
- http://www-sci.sci.ru.nl/xtal/dirdif/
Build-in:
10.
PLATON - Geometry Calculations etc.
11.
ORTEP - Stripped ORTEP
12.
SHXT86 - Stripped, Adapted & Modified old but powerful
SHELXS86/TREF.
13.
PLUTON - Molecular Graphics
14.
HELENA - CAD4-datareduction
15.
EXOR - Work-up/completion of raw E-map's
16.
ABSTOMPA - Exact correction for absorption
17.
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).
10.2 - Implementation Requirements
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:
- platon or PLAEXE for PLATON (Multipurpose Crystallographic Tool)
- shelxs or SHSEXE for SHELXS97 (Direct Methods)
- shelxl or SHLEXE for SHELXL97 (Least-squares Refinement)
- sir97 or SIREXE for SIR97 (Direct Methods)
- sir2002 or SR2EXE for SIR2002 (Direct Methods)
- dirdif or DIREXE for DIRDIF96/99 (Heavy Atom / Patterson Methods (Orient))