na PHAS reflections with Eo > Ek and the largest values of Ec/Eo are generated for use in partial structure expansion or direct methods. The first nH atoms (heavy atoms) in the atom list are retained during partial structure expansion, the rest are thrown away after calculating phases. At least one atom MUST be given! TEXP automatically generates appropriate FMAP, GRID and PLAN instructions.
TEXP (and/or PHAS) may be used in conjunction with TREF to generate fixed phases for use in direct methods; the special TEXP option na = 0 provides point atom phases for ALL reflections, which are then refined during the phase annealing and tangent expansion stages of direct methods (as specified on the PHAN and TREF instructions). It is not necessary to use different starting phases for the different phase sets, because the phase annealing stage itself introduces (statistically distributed) random phase shifts! This is a powerful method of partial structure expansion for cases when the phasing power of the partial structure is not quite adequate, e.g. when it consists of only one atom (say P or S in a large organic structure). If at least 5 atoms have been correctly located then TEXP alone should suffice.
When TEXP is used without TREF a tangent formula expansion (to all reflections with E > Emin as specified on the ESEL instruction) is first performed, followed by several cycles (see FMAP) of E-Fouriers and peak-list optimization. TEXP is particularly useful for cases in which several not very heavy atoms (e.g. P, S) have been located by PATT followed by hand interpretation of the resulting 'crossword table'. In such cases nH should be set to the number of such atoms and na to about half the number of reflections with E > 1.5 (see the first page of the SHELXS-96 output).
PHAS h k l phi
A fixed phase for structure expansion or direct methods. PHAS may be used to fix single phase seminvariants that have been obtained from other programs or derived by examination of the best TREF solutions. The phase angle phi must be present, and should be given in degrees.
atomname sfac x y z sof [1] U (or U11 U22 U33 U23 U13 U12)
Atom instructions begin with an atom name (up to 4 characters which do not correspond to any of the SHELXS command names, and terminated by at least one blank) followed by a scattering factor number (which refers to the list defined by the SFAC instruction(s)), x, y, and z in fractional coordinates, and (optionally) a site occupation factor (s.o.f.) and an isotropic U or six anisotropic Uij components (both in A**-2). The U or Uij values are ignored by SHELXS but may be included for compatibility with SHELXL.
When SHELXS writes the .res output file, a dummy U value is followed by a peak height (unless an atom type has been assigned by the program before the E-Fourier recycling). Both the dummy U and the peak height are ignored if the atom is read back into SHELXS (e.g. for partial structure expansion). SHELXL also ignores the peak height if found in the .ins file. In contrast to SHELX-76 it is not necessary to pad out the atom name to 4 characters with blanks, but it should be followed by at least one blank. References to 'free variables' and fixing of atom parameters by adding 10 as in SHELX-76 and SHELXL will be interpreted correctly, but SHELXL AFIX, RESI and PART instructions are simply ignored (so idealized hydrogen atoms etc. are NOT generated). The site occupation factor for an atom in a special position should be divided by the number of atoms in the general position that have coalesced to give the special position. It may also be found by dividing the multiplicity of the special position (as as given in International Tables) by the multiplicity of the general position. Thus an atom on a fourfold axis will usually have s.o.f. = 10.25 (i.e. 0.25, fixed by adding 10).
MOVE dx [0] dy [0] dz [0] sign [1]
The coordinates of the following atoms are changed to: x = dx + sign * x, y = dy + sign * y, z = dz + sign * z (after applying FRAG and SPIN - if present - according to PATSEE conventions); MOVE applies to all following atoms until superseded by a further MOVE. MOVE is normally used in conjunction with SPIN and FRAG (see below) but is also useful on its own for applying origin shifts.
TEXP may be used in conjunction with ESEL -1 for a partial structure expansion in the effective space group P1 (C1 etc. if the lattice is centered). This can be very effective if it is suspected that a fragment is correctly oriented but translated from its real position, or if the space group cannot be unambiguously assigned. Hand interpretation of the resulting E-map is then however necessary to locate the positions of the crystallographic symmetry elements.