SHELXT - small molecule structure solution
The new small molecule structure solution program SHELXT extracts the
Laue group, cell dimensions and types of element present from a SHELX
format .ins file, solves the structure using data expanded to space
group P1, and then uses the P1 phases to find the space group. In general
it produces a more complete solution than SHELXS or SHELXD and places the
correct absolute structure optimally in the unit cell. It ignores the
formula specified on the UNIT instruction and may even add elements if
that appears to be necessary. If the data are not as complete as required
for a Fourier based method like SHELXT (e.g. because a high pressure cell
was used) SHELXT simply invents the missing data (the free lunch
approach). SHELXT is highly parallel but the number of
CPUs used may be set using the -t command line option. SHELXT
requires two input files: an instruction file name.ins
and a reflection file name.hkl, and outputs possible solutions to
name_x.res and name_x.hkl (x=a,b,c...). A
summary is output to the console and a full listing to name.lxt.
SHELXT is started with the command line:
Exactly the same input files may be used as for SHELXS or SHELXD, but
all instructions between UNIT and HKLF are ignored. Many graphical users
interfaces (GUIs) and also the Bruker XPREP program may be used to create
these files. shelXle and other GUIs can also call SHELXT directly. The
Bruker version is called XT (or intrinsic phasing) but is otherwise
identical to SHELXT.
The Laue group deduced from SYMM can be overridden with -L followed
by the SADABS number for the Laue group (no intervening space); note the
special options -L15, -L16 and -L17. SHELXT reads
F-values rather than intensities if HKLF 3 is given in the name.ins
file. Only HKLF 3 and HKLF 4 are allowed but
the HKLF card may also include a reorientation matrix as for SHELXL. It is
assumed that the SFAC card correctly specifies the elements present, but the
numbers on the UNIT card are ignored. If the program thinks that a heavy atom
has been accidentally left out it may add bromine or iodine (orignally this
was an inert gas, but that would have led to a substantial increase in the
number of krypton structures in the CSD and COD). The program uses the
integrated electron density around an atom to assign the element type. This
is not very reliable, especially distinguishing between C and N, so the
assignments should always be checked carefully; the element assignment works
best with high quality complete data. SHELXT is no substitute for
SHELXT may stop when it thinks that it has a reasonable solution unless
is set to force it to try all space groups in the chosen Laue group. It is
advisable to input unmerged data (e.g. straight from SADABS),
otherwise there may be problems with the Flack parameter. The program will
a solution if the Flack parameter is greater than 0.5. Although the Flack
parameter is not very reliable at this early stage, there has not yet been a
report of a case where it was necessary to invert the structure later.
The basic assumption made by SHELXT is that the structure consists of
resolved atoms. This is a very powerful assumption and it
enables the program to work with incomplete data from a high-pressure cell
or where the crystal did not diffract to high resolution.
However if the assumption of resolved atoms is not appropriate - e.g. in the
presence of twinning, severe or whole molecule disorder or modulation - other
methods such as charge flipping may be a better choice.
Command line switches for SHELXT
The following list of command line switches is output when SHELXT is started
without a data file. Default settings are given in square brackets.
-L Laue group N (SADABS code). N=15 all hexagonal and trigonal,
N=16 monoclinic with a unique, N=17 monoclinic with c unique.
If -L is not set, the SYMM instructions set the Laue group.
-tN use N threads, otherwise use 4 or max available, if less. This
applies only to the P1 solution stage, for the other calculations all
available threads are used.
-d highest resolution to be employed [-d0.8].
-e fill out missing data to specified resolution [-eX
where X is max(0.9,d-0.1) and d is the resolution of the input data after
possible truncation with -d].
-q structure factors Go=EqFo(1-q)
map in dual space recycling [-i3]
-o switch OFF Patterson superpostion (not recommended).
-kN apply random omit every kth cycle [-k3].
-fX randomly omit fraction X of atoms [-f0.3].
-z sigma threshold for P1 peak-search [-z2.5].
-uX tangent expansion for E>X after random omit [off].
-v atomic volume threshold in Ångstroms for P1 peak-search
-m initial number of P1 dual space iterations [-m100].
-b spread factor for atom masks [-b3].
-jX CFOM = 0.01*CC - X*R(weak) [-j1].
-y CFOM = Chem*CC (alternative to default -j1) [off].
-xX accept if CFOM > X+0.01*max(20-m,0) where m is the
try number [-x0.65].
Chem is a 'chemical' figure of merit that should be between 1.0
(most reasonable) and 0.0 (awful). Currently the only option (-y
or -y1) is the fraction of bond angles between 95 and 135 degrees
ignoring the 20% highest and 10% lowest peaks. This is only useful for
organic compounds, organometallics and ligands, not for inorganics, but
can be invaluable when CC and R(weak) fail to distinguish
between correct and incorrect P1 solutions.
Space group determination:
space group (replace "/" by "_" e.g. -s"P2(1)_c") [off].
-c space group restricted to the Sohncke space groups [off].
-n space group restricted to non-centrosymmetric [off].
-w worst alpha gap for a possible solution [-w0.15].
-p maximum number of atoms in full matrix, rest are blocked
-g smallest gap in R1 to best cent. for non-cent. SG
-h halt if R1 is less that this [-h0.08].
-r radius around peak for density integration [-r0.7].
-aX search ALL space groups in given Laue group with alpha < X
-a overrides -g, -h and -w, but
not -c or -n;
-a without a number is equivalent to -a0.3.
If the default settings fail, try -y and -a. If the CC
is good but the solution is a mess or if all the CC values are
less than 0.87 try -m1000. Also well worth trying is truncating
noisy outer data stepwise with -d. When the program produces more
than one possible solution, the following criteria should be checked:
1, Is R1 low enough, taking into account that a slightly lower value
may result if the space group is a lower symmetry subgroup of the true
2. Has the program tried to throw in unexpected iodine or bromine atoms?
This is usually a bad sign, unless they are really there of course!
3. For a non-centrosymmetric solution, a Flack parameter close to 0.5 may
indicate that it is really centrosymmetric. A negative Flack parameter
may be caused by a wrong element or wavelength (common for synchrotron
data). However at this early stage, the Flack parameter is not always