Chapter 7 - Contoured Difference Maps
Five types of Fourier maps are contoured
- Fo Map : F(obs) Fourier with phases from F(calc)
- 2Fo - Fc Map : 'F(obs)' Fourier with phases from F(calc)
- Fo - Fc Maps - Difference Fourier with phases from F(calc)
- SQUEEZE Maps - Fo - Fc Map of density on VOID. F(obs) phases from model and
solvent
contributions, F(calc) phases from model.
-
Patterson Map
Structure factors are calculated based on the model in the '.ins' file.
OMIT instructions prior to the map calculation allow for the omission of the named atoms
from the structure factor calculations.
Example : 'OMIT O1 O2'
Scattering factors used in the calculations are indentical to those used by SHELXL97.
Introductory Example
I
n order to draw contour maps two data files will be required.
1. A file containing the structural parameters.
This can be a
- A SHELXL
.res style structured parameter file
- A
.cif style structured Crystallographic Information File
- A
.spf style standard parameter file.
2. A file containing reflection data.
This can be a
- A standard SHELX
.hkl structured reflection file (HKLF 4)
Note: to be used in combination with a .res (with HKLF 4 line)
- A standard SHELX
.fcf reflection CIF.
Example data for the worked example, C10H12O6, given below are
cdemo.cif
and
cdemo.fcf
Invoke PLATON with these two files with
platon cdemo.cif
Click on the PLATON opening menu on the option 'CONTOUR-Fo'.
Three points can now be entered to specify the desired general plane in the Fourier map to
be contoured.
As an example enter the points O501, C501 and O502 respectively.
The result of the calculation is shown in
Fig. 1
The menu on the right side of the plot now gives various option for subsequent plots.
The next layer (0.3 Angstrom above the previous one will be shown by clicking on the 'Up'
button.
Chapter 8 - PLATON/CHECK Build-in Structure Validation
X-Ray crystallography has rightly the name of providing SOLID information on molecules
in the crystalline state. However, the often forgotten condition to justify such a label for a
particular instance of a crystal structure determination is that the underlying procedures
should have been carried out adequately and correctly. Unfortunately, that turns out to be
not always the case. Major causes are related to lack of experience in picking up signals
indicating problems. Objective validation procedures attempt to address a large number of
potential problems as a routine procedure (see Spek (2003) & Spek (2009)).
An excellent paper by R.L. Harlow, detailing many of the issues involved, can be found in J.
of Research of the National Institute of Standards and Technology, (1996), 101, 327-339.
Troublesome Crystal Structures: Prevention, Detection, and Resolution.
Structural data provided in CIF-format (or CCDC-CIF format) may be validated in terms of
consistency, missing relevant data, proper procedure and overlooked problems.
In addition, reflection data will be validated on completeness and missed twinning effects
when provided with an FCF file. For documentation
see
.
PLATON implements a large variety of such tests specified in
check.def
The PLATON validation test set includes many of the official IUCR Validation Procedures
in use for the validation of Acta Cryst. papers reporting single crystal structures.
This set is complemented with a more involved analysis of the data themselves with
techniques available in PLATON (ADDSYM/VOIDS/Thermal Motion Analysis etc.)
I
t should be realized that validation has at least three faces:
- Checking for omissions & obvious errors.
Refined structures should be routinely checked for these problems prior to
submission to a journal.
Common problems include misplaced hydrogen atoms.
- Pointing to technical issues to be discussed in some detail
This includes a discussion on issues related to pseudo-symmetry, disorder etc.
- Pointing at unusual but potentially interesting structural features.
This includes interesting short intermolecular contacts.
Note: A subset of the the validation checks is applied for CCDC-FDAT structured files.
Implementation
The validation feature in PLATON may be invoked in three ways:
1. via the VALIDATION button on the PLATON-Opening window.
2.
via: 'platon -u data.cif' (or
-U for no validation documentation)
3. with instruction 'VALID' from the keyboard
In all cases, a copy of the file 'check.def' should be present in the current directory.
Alternatively, the path to check.def may be given via the environment variable
'CHECKDEF'.