How-to-Use SQUEEZE


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

PLATON/SQUEEZE offers an essentially blackbox tool for the handling of the contribution of the disordered solvent part of a crystal structure to the calculated structure factors as part of the least-squares structure refinement procedure using the refinement program SHELXL (Preferably 2019/3 and later).

Please Note: PLATON/SQUEEZE does NOT do a model parameter refinement, i.e. the coordinate and displacement parameter values are not changed. The latter is done only with the subsequent SHELXL refinement using the solvent info in the .fab file as created by PLATON/SQUEEZE.

The PLATON/SQUEEZE tool takes as input the files name.cif and name.fcf of a preliminary converged SHELXL based refinement of a model without the solvent contribution. It automatically generates three new files (name_sq.ins, name_sq.hkl and name_sq.fab) that can be used for the final refinement with SHELXL. The name_sq.fab file includes the solvent contribution to the structure factors along with details of the PLATON/SQUEEZE calculation. The name_sq.hkl file is a copy of the .hkl file embedded in the name.cif file. The name_sq.ins file is essentially an edited copy of the name.cif embedded .ins file. In addition, a file is created that illustrates the effectiveness of the SQUEEZE tool for this particular input data when run in the '-q' mode (vide infra). The latter info is displayed automatically when SQUEEZE is run in the interactive mode.

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

For more information please also consult the powerpoint presentation

SQUEEZE can be invoked in the non-graphical automatic execution mode with the instruction platon -q name.cif or in the graphical interactive mode with its invocation as platon name.cif followed by clicking on the SQUEEZE option on the PLATON main menu.

Alternatively, there is also the interactive input instruction (to be entered at the bottom after '>>':
SQUEEZE (PROBE radius[1.2]) (PSTEP nstep[6]) (CYCLE ncyc[25])
The SQUEEZE default settings 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 points are separated by about 0.2 Angstrom. By default, the back-Fourier transformation is recycled up to 25 times.

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.

The SQUEEZE method relies heavily on the quality of the low-order reflections. The dataset should be as complete as possible. Systematic errors may hamper the quality of the results

Large voids may require significant computing time 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 in the source code, to a larger value and recompile).

The number count of recovered electrons in the solvent area is strongly dependent on the quality of the low-angle reflections. Supply complete data sets, otherwise that count can be meaningless.

Applicability conditions:(1) Reasonable data resolution (i.e. sin(theta)/lambda at least 0.6 ang^-1), (2) The host (modelled) part of the structure complete including hydrogen atoms, (3) The solvent density should be well outside the modelled host part of the structure (i.e. not overlapping with significant host disorder), (4) The volume to be SQUEEZEd should not be too large (say less than in the order of 30% of the unit cell volume)

20-sep-2023, A.L.Spek