How-to-Use SQUEEZE


VOID TOOLS PLATON HOMEPAGE

Note: The SQUEEZE procedure has now been changed to make use of the new functionality provided by SHELXL2014 and up for structure refinement. The latter eliminates the need of working with solvent removed HKL files and also allows for twinning to be taken into account.

The current recommended input files are the SHELXL2014 based name.cif & name.fcf with output files name_sq.hkl & name_sq.fab for follow-up SHELXL2014 refinement

The original name.ins + name.hkl input in combination with SHELXL97 or SHELXL2013 still works but discouraged.

For more information please consult the powerpoint presentation

Paper: PLATON SQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors


SQUEEZE: An effective cure for the disordered solvent syndrome in single crystal structure refinement.

General

See Abstracts:

The SQUEEZE procedure takes care of the contribution of a (heavily) disordered solvent to the calculated structure factors by back-Fourier transformation of the continuous density found in a masked region of the difference map. The masked region is defined as the solvent accessible region left by the ordered part of the structure.

The current version of SQUEEZE has been designed, dimensioned and tested for small moiety structures containing disordered solvent molecules of the type toluene, CH2Cl2, tetrahydrofurane, water, methanol etc.. Anions such as ClO4-, PF6- etc. may be treated in the same way. However, take care of the problem of uncertainty of charge balance.

Large voids may require significant computing in the stage where the size and shape of the solvent accessible void is determined. All calculations are done in the triclinic system (data are expanded automatically when appropriate). Reflection data and FFT-array are stored in memory i.e. large structures (and high symmetry) may require large amounts of memory (change parameter NP21, that defines the available scratch area, globally to a larger value).

Implementation and Use:

SQUEEZE has been implemented as the 'SQUEEZE option' in the program PLATON.

PLATON/SQUEEZE should be compatible with small-moiety structure refinement usage of the popular program SHELXL-97 (or related incarnations).

The program is used as a filter. Input files are:

  1. shelxl.hkl - (HKLF type 4)
  2. shelxl.res - (complete set of refined model parameters, including hydrogen atoms but excluding any dummy atoms used to describe the disorder region)

invoke the program with:

platon shelxl.res

give on the prompt >> the instruction:

CALC SQUEEZE

or click on the main PLATON-menu option SQUEEZE.

The result will be in five files

  1. shelxl.lis: A listing file giving details of the calculations
  2. shelxl.lps: PostScript version of '.lis'
  3. shelxl.hkp: A modified reflection file against which the ordered structure parameters can be refined (the solvent contribution has been eliminated from the reflection data.)
  4. shelxl.sqz: Peak list of maxima found in solvent volume
  5. shelxl.sqf: SQUEEZE results in CIF format to be appended to the final refinement CIF for publication.

In order to run SHELXL-97 on the 'solvent-free' Fo^2 data:

(Note: save all files you want to keep)

- cp shelxl.res shelxl.ins

- cp shelxl.hkp shelxl.hkl

- run: shelxl

In order to get an .fcf style file (Fo^2 + Fc^2 (model + solvent)) you will need shelxl.hkl (= shelxl.hkp) and shelxl.res

run: platon shelxl.res

with the interactive option: CALC FCF

Final R-values are reported on the basis of the WGHT parameters in the shelxl.res file.

There will be a difference in reflection count as compaired to the SHELXL-run due to the differing number of surviving 'observed'reflections.

The procedure (starting from the original reflection data) can be repeated using the newly refined parameters when desired (This may define a 'refined' void area. However, there will be rarely a need to repeat the procedure).

The general procedure (based on a preliminary implementation of the technique) has been described in more detail in: Acta Cryst. (1990), A46, 194 as the 'BYPASS procedure' P. v.d. Sluis & A.L. Spek)

The 'difference-map' improvement potential of this technique has been demonstrated for small molecule structures. The technique should also work for protein data. However, this has not been tested by us as yet with PLATON/SQUEEZE. Current design features may cause problems when tried.

General SQUEEZE Keyboard Instruction

CALC SQUEEZE (PROBE radius[1.2]) (PSTEP nstep[6]) (CYCLE ncyc[25])

The default settings for the SQUEEZE options are generally adequate and correspond to the volume outlined by rolling a sphere with radius 1.2 Angstrom (i,e. van der Waals radius of a hydrogen atom) over the van der Waals surface of the ordered structure. Grid point are separated by about 0.2 Angstrom. By default, the back-Fourier transformation is recycled up to 25 times or when convergence id reached earlier.

Notes

Interpretation of the results

  1. A successfull application of SQUEEZE 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)
    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 peaklist should not contain significant peaks outside the VOID areas. Peaklist on .sqz file.

  2. Problems are indicated when

    1. Convergence is unstable
    2. A large number of reflections 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.

  3. A report on the use of SQUEEZE should always report for each (significant) independent void:

    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


VOID TOOLS PLATON HOMEPAGE
26-Feb-2021 A.L.Spek