1.3.3.3 – SQUEEZE – Handling of Disordered Solvent in the Refinement
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 out region of the difference map. The masked region is defined as the
solvent accessible region left unoccupied 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, CH
2
Cl
2
,
tetrahydrofurane, water, methanol etc.. Anions such as ClO
4
-, PF
6
- 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 where appropriate). Reflection data and the 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 is 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.
name.hkl - (HKLF type 4) or name
.fcf
2.
name.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 name.res
give on the prompt >> the instruction:
CALC SQUEEZE
or click on the main PLATON-menu option SQUEEZE.
Note: PLATON does some validation of the input data. It might happen that the program
stops with a message about too many atoms or ARU problems. In that case, issue the
command NOEXPAND before invoking SQUEEZE.
The result of a SQUEEZE calculation will be in five files
1.
name.lis: A listing file giving details of the calculations
2.
name.lps: PostScript version of
.lis
3.
name.hkp: A modified reflection file against which the ordered structure parameters
can be refined. The solvent contribution has been eliminated from the reflection data.
The original intensity is saved after colum 80 along with the solvent contribution to
Fcalc for later use (i.e. for CALC FCF –
Section 1.3.3.4 and CONTOUR SQUEEZE
-
Section 1.3.3.5)
4.
name.sqz: Peak list of maxima found in solvent volume
5.
name.sqf: SQUEEZE results in CIF format to be appended to the final refinement
CIF for publication.
The result of a SQUEEZE calculation can be used in two ways in the further refinement of
the structure: with a program such as Crystals (Watkin et al.) that accepts fixed contributions
to the structure factor calculation or with a program such as SHELXL97 that does not offer
this option by using the 'solvent removed' Fo^2 data. In order to run SHELXL-97 on the
'solvent-free' Fo^2 data: (Note: save all files you want to keep)
-
cp name.res shelxl.ins
-
cp name.hkp shelxl.hkl
- run:
shelxl
In order to get after convergence a proper .
fcf style file (Fo^2 + Fc^2 (model + solvent))
you will need
shelxl.hkl (=
shelxl.hkp) and
shelxl.res
and 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 might be a slight difference in the reflection count as compared 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 the paper on the 'BYPASS procedure' (van der Sluis & Spek,
1990). See also
Chapter 5.
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.
The 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 points are
separated by about 0.2 Angstrom. By default, the back-Fourier transformation is recycled up
to 25 times or when convergence is reached earlier.
Notes
- The record length of the '.hkp' file has been increased above 80 to
accommodate additional data
including the original intensity and calculated solvent contribution to the structure factors.
- The exact numbers on the SHELXL UNIT instruction are irrelevant for the SQUEEZE procedure.
- The SHELXL-TWIN instruction is not available as yet in PLATON. SQUEEZE is
currently not compatible with twinning.
- PLATON internally calculates structure factors (using the same scattering factors as used
by SHELXL97) for the model given in the
shelxl.ins file.
- The solvent contribution to the structure factors is taken as 'error-free'. This means that the
'solvent-free' Fo^2 keep their original su's (esd's).
- The method (in particular the electron count) relies heavily on the quality of the (strong)
low-order reflections. The dataset should be as complete as possible. Systematic errors may