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hamper the quality of the results.
- The Contour-Map option (
Section 220.127.116.11) in PLATON can be used to inspect the
improved difference-map (i.e. calculated with phases including the disordered solvent
- Current conditions for applicability are:
1. Reasonable data-resolution (say 25 degrees for MoKa)
2. Structure of the known part completed with H-atoms
3. Disorder density should be well outside the van der Waals surface of the
known structure. Exposed disorder may limit the applicability of the
4. The area to be 'SQUEEZE' should not be too large (say less than in the order
of 30% of the unit-cell volume.
Interpretation of the results
1. A successful application of SQUEEZE run will show the following results:
1. A new hkl-file against which a satisfactory refinement of the discrete model
can be done (purpose: good geometry, good R-value, insignificant residual
density excursions in the difference density map.)
2. Smooth convergence of the SQUEEZE iteration.
3. Significant improvement of the R-value in low resolution data. (see table at the
end of the listing file).
4. The number of electrons reported to be found in a void is close to that
expected for the assumed solvent.
5. The difference map peak list should not contain significant peaks outside the
VOID areas. Peak list is on .sqz file.
2. Problems are indicated when
1. Convergence is unstable
2. A large number of reflections is left out during the iteration process (This may
be well indicative for problems with the data, and should be checked for).
3. Large residual density excursions in the ordered part of the structure.
A report on the use of SQUEEZE should always report for each (significant)
independent void: (This can be done by appending the .
sqzfile to the final .
1. Where the void is (i.e. x,y,z)
2. Its volume in Ang**3 and multiplicity.
3. The number of electrons recovered.
4. Fo/Fc-listing with Original Fo and Fc including the solvent contribution.
Potential Problems and Pitfalls
- Be aware of charge balance problems: SQUEEZED density in the disordered solvent
area might contain a charge that can have consequences for the charge, valence and
interpretation of the ordered structure part.
- PLATON/SQUEEZE can take care of the redundancy of reflection data on the the
.hklfile. However, with high symmetry space groups this can lead to some
inefficiency and storage problems. It helps in such cases to supply an averaged, unique
dataset (Unfortunately, direction cosines will be unavailable in the latter case for post-
absorption correction; of-course a preceding numerical correction for absorption is to be
- The number of recovered electrons in the solvent area is strongly dependent on the
quality of the low-angle reflections. Supply COMPLETE data sets !
- Referees (and validation software) might wish to see details of the SQUEEZE
calculations. Those can be provided by appending the
.sqffile to the publication
18.104.22.168 - CALC FCF
Generation of the final Fo/Fc-Calculation/listing (SHELXL LIST 4 Style) for SQUEEZED
Required input files are:
1. shelxl.res: the final model refined against solvent free data
2. shelxl.hkl: the 'solvent-free' reflection file used in the final refinement.
The reflection .
fcfthat is produced in this way on the basis of the
reflection file will contain the original 'Fo**2' data (scaled on F(calc)) and F(calc)**2 data
as the square of Fc = Fc(model) + F(solvent). Fc(model) is calculated from the model in
Note: Prior to the output of the 'fcf' file, redundant reflection data are averaged and sorted
into a unique reflection file.
It might be profitable to average the reflection file used for SQUEEZE prior to the
SQUEEZE operation. A-priori averaging should be no problem when either absorption
correction is applied or not an issue for the particular dataset.
Note: In the non-SQUEEZE mode (i.e. with no data in the reflection record beyond column
80) the F(obs)**2 found before column 80 is used.
22.214.171.124 - CONTOURED SQUEEZE MAP
The 'SQUEEZE based difference map' may show improved features (in particular for non-
centrosymmetric structures) because it is calculated with better phases than those available for a
standard difference map. Files needed for the calculation are the
– SQUEEZE map. Enhanced Phases Difference Fourier section through the
disordered tetrahydrofuran molecule lying on a twofold axis.
126.96.36.199 – SOLV-F3D
A file (.slv) is generated with info on the solvent accessible volume for display with the program
F3D (Tooke & Spek, 2005). F3D is invoked automatically when accessible.
188.8.131.52 - SOLV – PLOT
Solvent accessible volumes in a structure may be detected using the PLATON/SOLV utility.
The PLOT option allows the graphical inspection of the solvent areas.
Two types of surfaces can be displayed:
1. The boundary of solvent accessible volume. This is the volume used with the
SQUEEZE algorithm to take the contribution of disordered solvent in that region to
the structure factors into account.
2. The boundary of the (smaller) 'Ohashi' volume. All points inside this volume are at
least 1.2 Angstrom away from the nearest van der Waals surface. See Ohashi et al.
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