The platon crystallographic package - səhifə 66
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- The supplied space group is used only to reflect the LAUE symmetry of the data set (thus
P2/m should do as well in this case). The latter is used to expand the (averaged) data to
- The scattering type of the first atom type given on SFAC is assigned to the atoms in
- The info on the UNIT line is used by the EXOR link to assign atom types to peaks.
- This routine is not optimized in terms of using the fastest available FFT routine (yet).
- The FLIPPER routine is currently experimental and under further development.
Preliminary experience learns that some structures come out easily and others of similar size
with great difficulty or not at all. Success or failure often depends heavily on the actual
choice of the
- A special Charge Flipping run is invoked through the
PATTentry on the main menu. The
structure is developed from starting phases set to zero.
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-Sis 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-Soperates as a supervisor (with a crystallographic degree and with an
organized memory) over the process of a single crystal structure determination by X-ray
- SYSTEM-Sprovides an interface to a variety of established datareduction, structure
determination, refinement and evaluation tools.
- SYSTEM-Sprovides 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-Sprovides 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 Sare either build-in (i.e. part of PLATON) or
external (i.e. plug-ins).
PLATON - Geometry Calculations etc.
ORTEP - Stripped ORTEP
SHXT86 - Stripped, Adapted & Modified old but powerful
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
SYSTEM-Scommands 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
- SYSTEM-Ssets 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-Srestarts, 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-Sis 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
- SYSTEM-Scomes as a build-in feature of PLATON.
- SYSTEM-Sis (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:
- platonor PLAEXE for PLATON (Multipurpose Crystallographic Tool)
- shelxsor SHSEXE for SHELXS97 (Direct Methods)
- shelxlor SHLEXE for SHELXL97 (Least-squares Refinement)
- sir97or SIREXE for SIR97 (Direct Methods)
- sir2002or SR2EXE for SIR2002 (Direct Methods)
- dirdifor DIREXE for DIRDIF96/99 (Heavy Atom / Patterson Methods (Orient))
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