The platon crystallographic package - səhifə 39
keyboard). By default, space groups in standard settings are suggested (resulting in a non
unit transformation matrix for the reflection data on the HKLF 4 shelx instruction).
Ssuggests a suitable space group based on several criteria, including the frequency in the
CSD and the optional additional information that the compound involved is chiral. An
alternative space group from the list can be selected either by clicking on the appropriate
line or explicitly from the keyboard. (E.g.
The alternare space group
P21/ncan be selected (keyboard instruction
SPGR P21/n) when
automatic transformation to P21/c is suggested but P21/n considered more suitable for the
current study (e.g to simplify the description of a twinning law). Note: Either P21/c or P21/n
can be chosen (i.e. not both).
184.108.40.206 - FORMULA & Z
FORMULA: The Formula instruction specifies the atom types and their number in the
molecule. Along with Z it determines the unit cell content. The formula can be changed
during the structure determination process. Elements can be added when needed.
FORMULA C 10 H 10 O 1
The latter format should be used to eliminate unwanted element types (either obsolete or
introduced as a type error).
Z: Z should be specified such that, along with the formula, it represents the unit cell
1. Reasonable Z values are guessed and could either accepted or superseded by the
2. In the absence of any prior knowledge of the contents of the unit cell the formula
(C1H2)n can be attempted in an attempt to solve a structure by Direct Methods (e.g.
220.127.116.11 - PLUTON & RENAME
Display and atom renaming functions.
18.104.22.168 - DIRDIF
PATTY:Clicking on this button invokes the DIRDIF/PATTY program suite for the structure
determination of 'heavy atom' structures via Patterson techniques.
ORIENT: Clicking on this button invokes the DIRDIF/ORIENT program suite for structure
determination based on an orientation search with a known structural fracment (model).
The model is assumed to be present as an ATMOD-file in ~USER/s/COMPOUND/.model.
When no such a file is found, the DIRDIF/ORBASE feature is started up in the ASCII
window in order to generate such a model.
1. Startup the sdemo test-example with SYSTEM S in space group Pc (or P21). Note:
P21/c will not work for the centrosymmetric model we are going to use.
2. Continue until the suggested 'shelxl86' based phase determination.
3. Click on ORNT (Next to the Dirdif field in the vertical menu at the right)
4. Answer the questions of DIRDIF/ORBASE. Choose either '19.11' (i.e. Benzene) or
18.11 (Benzoquinone) as a model. and save/exit.
5. A PLUTON drawing of the solved structure will pop-up.
6. Acknowledge the isotropic refinement instruction.
7. Click on ADDSYM to find out the real symmetry (P21/c). The result is shown on the
graphics window in RED: M/P-SPGR P21/c.
8. Implement the newly found symmetry by clicking on TRMX. As a result A new
branch in the directory tree is created up to the point where refinement can be
22.214.171.124 - SHELXS86, SIR97 & SIR2004
Clicking in one of the fields details below invokes a default run of the named programs to
(attempt to) solve a structure with the named program.
SHELXS86: Clicking on this button invokes a 'stripped' SHELXS86 version. A structure
solution by Direct Methods (TREF) is attempted.
The resulting 'raw' peak list can be 'cleaned' with one of the 'exorciser-tools' EXOR,
EXORS, EXORD or EXORC.
SIR97: Clicking on this button invokes the SIR97 (Direct Methods) structure determination
SIR2004: Clicking on this button invokes the SIR2004 (Direct Methods) structure
126.96.36.199 - EXOR, EXORS, EXORD
EXOR: Automatic work-up of raw model (e.g. from Direct Methods, SHELXS/PATT) to a
more complete model with automatically assigned atom-types. The EXOR(cise) procedure
is based on a sequence of population parameter refinements and difference maps.
EXORS: Automatic work-up of raw model (e.g. from Direct Methods) to a more complete
model with automatically assigned atom-types. The EXORS procedure is based on a
sequence of displacement parameter refinements and difference maps (using SIR).
EXORD: Automatic work-up of raw model (e.g. from Direct Methods) to a more complete
model with automatically assigned atom-types. The EXORD procedure is based on the
PHASEX procedure in DIRDIF.
188.8.131.52 - SHELXL-ISO
Clicking in this field will start an isotropic displacement parameter + coordinates refinement
Features and Options
- The click position determines the number of least-squares cycles [0:5].
- The leftmost button (0 cycles) gives a structure factor and difference map calculation
only, suitable for structure completion from a preliminary model.
- Setting the toggle 'EDIT-SHXins' gives access to the input file to SHELX prior to
launching the actual calculations, allowing for setting any special desired non-standard
features using a text editor.
Calculations start automatically after termination of the editor.
184.108.40.206 - SHELXL-ANISO
Clicking in one of the six boxes will invoke an anisotropic displacement parameter
refinement with 0 to 5 cycles. Isotropic displacement parameters for non-H atoms are made
220.127.116.11 - TwinRotMat
Detection of missed twinning. See
Chapter 6for details.
18.104.22.168 - HDIF & HFIX
HDIF: Hydrogen atom position pick-up from a difference map followed by population
HFIX: Introduction of hydrogen atoms via the SHELXL/HFIX mechanism.
22.214.171.124 - SHELXL-HATS
Refinement including H-atoms (either riding or free)
126.96.36.199 - SHELXL-WEIGHT
Refinement with weights including weight optimization. Additional refinement cycles are
suggested until convergence is reached.
188.8.131.52 - PLUTON & RENAME
Display and atom rename functions.
See for details
184.108.40.206 - PLATON & ADP
PLATON:Facilities:This Option brings up PLATON for additional Tools using the current
CIF-data is input (or .res when
.cifis not available).
ADP: Clicking in the rightmost box (ADP) brings up the build-in ORTEP function in
220.127.116.11 - INVERT & HFREE
INVERT:Inversion of the Absolute Structure
Non-centrosymmetric structures may require inversion of the structure in
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