Recent SHELX changes
The new small molecule structure solution program SHELXT
has been released. It will in general give a more complete solution than
SHELXD or SHELXS, but SHELXD is still recommended for very large
equal-atom or twinned structures. SHELXT can read the same name.hkl
and name.ins files as SHELXD or SHELXS, and is started from a
command line by:
SHELXT solves the structure by a novel dual-space method using data
expanded to P1 and then uses the P1 phases to determine the space group.
It only requires the cell dimensions, Laue group and a list of elements
present; this information is extracted from the .ins file. The
program is highly parallel and runs well on multiple-CPU
computers. Further options are available via command-line switches, but
except for
Recent changes are listed below, with the
most recent changes in each program first. A PDF discussion of the
extensive changes in the 2013 release of SHELXL relative to SHELXL-97 may
be found here.
The SHELXL-2013 CIF files containing embedded .hkl and .res are now accepted for papers submitted to Acta Cryst. and many other journals, and also by CheckCIF, PLATON, the COD and the CCDC. In accordance with IUCr policy, the .hkl file should not be merged before reading into SHELXL because this prevents SHELXL from calculating some of the numbers needed for the CIF file. A LIST 4 .fcf file is apparently still required by the IUCr but not for the PLATON implementation of CheckCIF. The .fcf files have the disadvantage of being merged in a particular point group and having had their systematic absences removed, making it more difficult to verify the correctness of the space group, so their use for archiving and publication purposes should be deprecated.
The Bavarian State Library has very kindly put some SHELX-relevant papers onto its Open Access Leibniz portal. Click on 'Sheldrick' to find them. To avoid possible misunderstanding, I should add that Göttingen is not in Bavaria and there are no plans to move it there.
Version 2016/1
1. A serious problem involving the merging of intensity data that was
introduced in version 2015/2 has been fixed.
Version 2015/2
1. The diagnostic tables have been extended to include the reflection
multiplicity, R(pim) and R(anom).
2. For a SAD experiment, SHELXC writes a file name_sad.cif. This may
be converted directly to a mtz file using the CCP4 utility cif2mtz, and
contains merged native data, anomalous differences and free_R flags. The
SHELXC instruction 'FREE 5' (the default if no FREE instruction is given)
would specify that 5% of the reflections, chosen at random, should be
flagged for use in calculating the free R. 'FREE -7' would flag 7% in thin
shells. If a reflection is present in the SAD data but not in the NAT data,
it is scaled and included; this improves the comleteness of the native data
and is useful when a shorter wavelength for NAT compared with SAD causes
some low angle reflections to be missing from the NAT file.
3. All recognized SHELXD instructions input to SHELXC are now written to the
name_fa.ins file for use by SHELXD.
Version 2014/2
1. A serious error in calculating the completeness has been fixed. The effect
was to count all systematic absences as if they were in the inner resolution
shell, whatever shell they should have been in. Other calculations were not
affected by this.
Version 2014/1
1. A formatting error in the command summary output when SHELXC is started
without command line parameters has been corrected.
Version 2013/1
1. The statistics output has been improved for low resolution data.
2. When (e.g. for MAD or SIRAS) more than one dataset is read in, SHELXC
checks that they have been indexed consistently and if necessary re-indexes
the data as required, in which case some extra output appears. If native data
are read in, they are used as the standard for indexing. The check is not
exhaustive but should cover all common cases.
3. As a quick check on possible twinning, <|E²-1|> is output for each
dataset.
Version 2013/2
1. Change 2 in version 2013/1 had the unfortunate side-effect of stopping
prematurely if NTRY wasn't specified. This has now been fixed, if NTRY is
not set, the program runs for ever, as specified in the documentation.
It can however still be terminated by creating a .fin file with the
same first name in the directory in which the program is running.
Version 2013/1
1. Multiple CPUs are now always used if available, there is no special
shelxd_mp version.
2. Previous versions divided the number of trials (NTRY)
equally between the different threads. If other programs were also running,
this could result is one or more threads taking appreciably longer than the
rest to finish. The trials are now distributed dynamically so that all threads
finish at about the same time, making the program even faster.
Recent versions of SHELXE contain major contributions from Prof. Isabel
Uson (Barcelona).
Version 2018/2
1. NCS derivation from HA sites (-n) should now work again properly, in
the 2017 versions it was missing from the command summary and
occasionally caused a segmentation fault. In the 2018/2 version it is
robuster and much faster. It is recommended that NCS is specified simply
by e.g. -n6 for the CCP4 gere test that has six-fold proper NCS for a
total of 12 heavy atoms). The alternative -n206 (see recent change 2014/3)
still works but has no real advantage and if there are many heavy atoms
it can be much slower.
2. A bug ocasionally affecting -K, that led to atoms in the fixed fragment
being wrongly labelled or lost, has been removed.
3. A bug afecting atom weights in seed refinement has been fixed.
4. Helical geometry at low resolution is idealised in -Q (typically
useful for coiled coils).
Version 2018/1
1. The chain tracing algorithms have been improved and should now work
better at low resolution.
2. The expiry date is currently 1/1/2019.
Version 2017/1
1. -a without a number performs up to 30 global tracing cycles, but stops
three cycles after the CC value has gone above 30% if that happens earlier.
2. When a .pda file is read, the default value of the command line
option -v changes to -v0.
3. The options -O and -Z for rigid group refinement of an input fragment
have been withdrawn, this is better performed by a molecular replacement
program.
4. If -x is set (to compare the phases with phases generated from a reference
PDB file) the reference structure in the .ent file is also used to
estimate the solvent content and the percentages of alpha-helices and
beta-strands.
5. Another bug in calculating the origin shift for certain rare cubic space
groups using -x, introduced in version 2016/3, has been fixed.
6. The program should now produce identical phases etc. whether or not -x
is set.
7. -z seems to be performing erratically and so should be used with caution.
8. The program should no longer terminate with the message that a peptide
occupancy has become negative.
9. When the -o option is used to improve a trial structure by eliminating
residues, and NCS copies are defined in the .pda file, the same changes
are made to each NCS-related fragment.
10. The command line option -q (default -q7) accepts values between -q7 and
-q14 to seed main chain tracing with polyalanine helices of 7 to 15 amino acids.
The longer helices and restrained refinement are intended for tracing
structures at resolutions below 2Å.
11. The command line option -Q, to be used instead of -q, constrains helical
extension of helical seeds in all cycles but the last. This is intended for
tracing coiled coils at resolutions below 2Å.
12. The command line option -B uses two-stranded beta sheets to seed main
chain tracing. -B1 uses antiparallel, -B2 parallel and -B3 both kinds of
template. This is intended for tracing structures with beta sheets at
resolutions below 2Å or starting from poor phases.
Version 2016/3
1. The expiry data has been extended to 1/1/2018.
Version 2016/2
1. The calculation of the mean phase error using the -x option sometimes
gave the wrong answer for the not very common space group F23. This has
now been fixed, other space groups should not have been affected.
2. A serious error in the MRSAD calculation (with name.pda and name_fa.hkl)
has been fixed.
Version 2016/1
1. SHELXE traces from CA to CA but had been counting the ends as separate
residues, with the result that the number of residues per chain was one too
high. This has been corrected.
2. The output .pdb file has been tidied up. The heavy atoms used for
phasing (if -h is set) now come first but are put in chain Z. The traces
are put in chains A to Y (except when -K is set, then the atoms from the
.pda file are all in chain A). The chains are sorted so that the
longest are given first. If there are more chains that this allows, the
remaining short traces are packed into chain Y with a one residue gap
between separate chains.
3. Several small bugs have been fixed.
Version 2014/4
1. The density modification has been improved for SAD phasing. For 20 test
structures, this led to an average improvement of about four degrees in the
mean phase error.
2. An error in counting residues in the final output .pdb file has
been corrected.
3. NCS may now be specified in the .pda file to trace from a partial
structure:
should be inserted before each monomer. The monomer is terminated
by the next such GROUP BEGIN record or by:
Each monomer should contain the same atom names in the same order, but
the chain IDs and residue numbers may differ. The NCS operators are deduced
from the coordinates of the monomers in the .pda file and are applied
during tracing. The
Version 2014/3
1. The
2. The 'on the fly' calculation of the origin shift and mean phase errors
using
3. For experimental phasing the origin shifts are also used to
identify which atoms in the reference .ent
file are closest to the heavy atom sites, taking symmetry into account.
Version 2014/2
1. The new -K option was causing the new trace to overlap the input fragment.
Now the NOGO map is used to prevent this from happening.
2. The program was unintentionally not accepting -k. This has been corrected.
3. The -B option has been removed, it did not work correctly anyway.
Version 2014/1
1. -zN limits the total number of heavy atoms to N, previously in borderline
cases it tended to add too many noise peaks.
2. -IN does N cycles density modification on global cycle 1 using free lunch
reflections if set by -e. Subsequent cycles use the -m setting as before.
In cases suitable for a free lunch one could try e.g. -I200 or more.
3. -KN keeps the starting fragment for the first N global cycles, after that
it is thrown away. If -K is given without a number or that number is larger
than -a, the initial (pruned) fragment is also still output to the .pdb.
The fragment does not have to be a polypeptide.
Version 2013/3
1. A number of small improvements have been made, affecting both experimental
phasing and expansion from a MR solution. In some cases these may make the
difference between solving a structure or not!
2. If -x is specified and a PDB format file with the extension .ent is
provided, mean phase errors (MPE) and weighted mean phase errors (wMPE) are
calculated separately for all and for centric reflections. In addition the
alpha carbon positions are compared with the reference positions. The
necessary origin shifts are found 'on the fly' using an algorithm that
should be efficient for all space groups. It is still necessary that the
reflection data are indexed consistently with the coordinates in the .ent
file (in space groups like P31 etc.).
3. For experimental phasing both -z (to refine the heavy atoms) and -n (NCS)
should be used whenever applicable, The NCS operators are derived from the
heavy atom positions after they have been refined. Note that NCS is
currently only applied when the operators can be deduced from heavy atom
positions, not when starting from phases or a MR solution.
Version 2013/2
1. Several serious problems affecting MRSAD and expansion from a MR model,
that were present in the last beta-test version 2013/1, have been fixed.
A new program PDB2INS written by Anna Lübben is now available for
converting PDB files to .ins files for input to SHELXL. It uses the
new facility in SHELXL for chain-IDs, so the same residue numbers may
be used in SHELXL as in other refinement programs. It also automatically
inserts DISP instructions and the required geometrical restraints, and
tries to handle insertion codes etc. It can download the PDB and reflection
data (if available) directly from the PDB. About 95% of the X-ray structures
deposited in the PDB since 2008 can then be refined directly with SHELXL
without needing to edit the .ins file created by PDB2INS.
Version 2018/3
1. When the last digit of an AFIX or HFIX code is 8 (e.g. AFIX 148), the
entry in the CIF file is now always '_refine_ls_hydrogen_treatment
mixed'. Previously it could have the value 'constr', which CheckCIF
punished with the draconian Alert A.
2. A technical error has been corrected that often appeared to have no
effect but sometimes resulted in a segmentation fault.
3. Errors have been corrected in the default scattering factors for the
elements Cf and Bk. Other elements were not affected.
4. The new instruction 'PAIR d' calculates R1 and R1(free) for data
up to a resolution of d Angstroms, but all the data within the limits
imposed by SHEL are still used for refinement. The R1 and R1(free) from
such a paired refinement may be used to decide at which resolution
to truncate the data with SHEL ['paired refinement', Karplus & Diederichs
(2012) Science 336, 1030-1033].
5. The default TWST value has been changed from 0 to 1. This enables the
Friedel coverage to be calculated 'correctly' for a TWIN or HKLF 5
refinement.
6. The tags ^a etc. to indicate PART numbers are not longer output to
.cif files unless the TAGS keyword is used on the ACTA
instruction. Note that CIF format does not allow atoms to have the same
atom and residue names but SHELX, PDB and mmCIF formats do allow this
provided that they have different PART numbers (alternative site flags
in PDB format), which greatly simplifies the use of restraints for
disordered residues and enables shorter atom names to be used. As a
result, SHELX users should only use atoms
with the same atom and residue names for macromolecues that will be
deposited with the PDB, not for small molecules that require a CIF
file to be deposited.
Version 2018/1
1. SAME_XYZ was sometimes incorrectly using residue 0 as well as residues
XYZ. This should no longer happen.
2. A problem involving the use of chain-IDs with SAME has been fixed.
3. A restraint such as SIMU_XYZ only affects atoms pairs where both atoms
are within the same residue of type XYZ, not atom pairs involving two
different residues. This is necessary for the program logic but has
caused some confusion.
4. Because of the extra space taken by chain IDs and PART numbers
displayed as ^a etc. changes had to be made in several places. primarily
in error messages, to prevent possible buffer overrun.
5. In the long deprecated 'lineprinter plots' (PLAN -N), the symmetry
equivalent code has been reinstated and the output tidied up a little.
6. Some time ago, to avoid misleading error messages, FREE and BIND were
changed to accept two and only two atom names.
Version 2017/2
1. Scattering factors are now stored for all elements up to and including
californium (Cf). For other elements it is still necessary to use the long
form of the SFAC instruction.
2. Input lines longer than 80 characters were truncated to 80 on input,
with unpredictable results. A fix for this in version 2017/1 had problems
when column 80 was being used for something sensible. The method of
recognizing this situation has now been improved and a warning should now
appear only for lines that are really longer than 80 characters.
3. RIGU normally generated three restraints for each atom pair. In version
2017/2 the restraint for motion along a line joining two atoms (denoted
zz) is not applied if the atomic numbers of the two atoms differ by more
than three units, but the other two restraints that enforce relative motion
perpendicular to the line are still applied. For technical reqasons, if
NEUT is specified all three RIGU restraints are applied as before.
It is still possible to restrain the relative motion along this line by
using DELU.
4. It should no longer be possible to generate an empty CIF loop which
would break the CIF syntax, e.g. when there are no bonds linking
non-hydrogen atoms (this is actually a design weakness of CIF, because
CIF has no 'end of loop' flag). However H-bonds may still be calculated
in such cases using HTAB, e.g. for ice or solid ammonia.
5. Zero length bonds on SADI instructions are now treated as errors; they
are invariably typos.
6. The allowed number of $n codes for symmetry operations (used e.g. by
HTAB) has been increased to 999.
7. A BIND instruction may be used to force the inclusion of specified
bonds to hydrogen atoms into the connectivity table so that they are also
used in the output of geometrical parameters; e.g. BIND O2 H2. This may
be useful for large structures where BOND $H creates a large amount
of output.
8. Restraints etc. involving _+ and _- should now always be applied if
specified, in previous versions they were sometimes ignored.
9. Several other very minor problems have also been tidied up.
Version 2017/1
1. The range of allowed residue numbers is now from -999 to 9999. This was
needed for files generated by pdb2ins because PDB files often contain
negative residue numbers for e.g. N-terminal His-tags.
2. Residue names may now begin with a digit, since this is also allowed
in the PDB. They must however contain at least one letter so that the
program can distinguish them from residue numbers.
3. The action of a global SAME instruction such as
4. The generation of the output PDB file with
5. If there are no hydrogen atoms in the structure,
6. _geom_hbond_publ_flag has been added to the hydrogen bond table generated
by
7. Duplicate atom names are now always named correctly in the corresponding
error message.
8.
9. The -c command line parameter was being interpreted wrongly, resulting
in an error mesage. It should now work correctly. In any case this option
is very rarely needed.
10. The list of possible hydrogen bonds generated by
11. An instruction like:
12. Angles involving different components of an AFIX 12N disordered methyl
group should no longer appear in the CIF file.
13. The CIF output of AFIXed hydrogens attached to atoms on special
positions has been tidied up and duplicates removed.
14. For the final structure factor calculation for non-centrosymmetric
structures, for many years the program has been reporting the number of
parameters refined as 2 instead of the correct value of 0. This is possibly
a hangover from a previous method of estimating the Flack parameter. It is
now reported as 0 for both centrosymmetric and non-centrosymmetric
structures.
15. The FREE instruction should now work properly when the second atom is
a symmetry equivalent.
16. The LIST 8 output includes both normal and free-R reflections. A new
option LIST 9 now lists the free-R reflections only, and LIST 10 lists
only the non-free-R reflections. LIST 8, 9 and 10 use the same format.
17. Instructions in the .ins file that were longer than 79 characters
were being truncated on reading them in. Such instructions now give rise to
an error message.
18. RESI 0 is predefined to have a blank residue name and this is the
default until a RESI instruction is encountered on reading the .ins
file. An attempt to reset RESI 0 with a different name caused problems and
is now forbidden.
19. Improvements have been made to the handling of SADI, ISOR, NCSY and
CONN.
20. ^a, ^b etc. should now appear in the connectivity table as required.
21. Residue names but not chain IDs are converted to upper case on input.
22. The memory allocation for the parallel part of the code has been
reorganized to make it more efficient and robust.
23. The list of times for different operations should now be more accurate
for multithreading. This required combining the times for structure factor
calculation and building the least-squares matrices (since these operations
may be performed simultaneously by different threads), but the time for the
final structure-factor calculation is now output separately.
24. HTAB without any atom names should now generate EQIV and HTAB
instructions for all hydrogen bonds including ^a, ^b etc. to specify PART
numbers as required.
25. Only one pair of atoms may now be specified on each FREE or BIND
instruction. This avoids problems caused by missing atoms when many such
instructions were combined in a single line.
Version 2016/6
1. A format error in the output PDB file has been fixed, TER inserted at
the end of each chain and element names included in columns 77/78.
2. The 'time stamp' at the start of the .res file still caused
problems for some vintage programs. It has to follow the TITL instruction
because apparently some programs assume that a SHELX .res file must
begin with TITL (actually TITL was always optional). Using a REM comment
would cause these lines to accumulate each time SHELXL is run, and a comment
starting with one space, although SHELXL standard for many years, also
upset some vintage programs. The 'time stamp' now immediately
follows TITL and consists of two lines (to avoid problems with very long
filename paths) each beginning with four blanks.
3. The HTAB and EQIV instructions created for re-input by a HTAB instruction
without any parameters were sometimes missing EQIV instructions. This has
been fixed, but please note that existing EQIV instructions should not be
removed or modified when using this facility.
4. ANIS instructions were sometimes not working, this should now be better.
5. R.m.s. bond length and angle deviations, required by certain journals for
the notorious 'Table 1' for macromolecular structures, are estimated using
the DFIX and DANG restraints.
6. In the 'recommended weighting scheme' (see item 7 for 2016/5) by popular
request the threshold for g has been changed back to 0.2, and the refined
value is also output for information if it is above this threshold. Refined
values above 0.1 usually indicate poor quality (or macromolecular) data.
7. Generally the instructions in the .ins file are not case
sensitive. However an exception is made for the ChainIDs (see item 2 for
2016/4) that as in the PDB now distinguish between upper and lower case
letters, allowing up to 63 different chains (this was not implemented
properly in versions 2016/4 and 2016/5).
Version 2016/5
1. The appending of '_a' or 'b' etc. for atoms with different PART numbers
was potentially ambiguous and has been discontinued. It may still be
necesary to refer to an atom with a specific PART number when there are two
or more atoms with the same atom name and residue number but different PART
numbers, e.g. when two such disorder components make hydrogen bonds to
different atoms. This may now be done by ^a, ^b etc. before or after the
residue identifier, for PART 1 and PART 2 respectively, e.g. C1_2^b. If all
the disordered atoms have different names or residue numbers this is no
longer necessary. When this facility is not used the restraint etc. is
applied to all atoms with matching names and residue numbers. Because of
this change, the symbol '^' may no longer be used in an atom name.
2. Some of the EQIV instructions generated by HTAB in version 2016/4 were
incomplete and there was a superfluous symmetry operator in the list of
hydrogen bonds in the .cif file. Both have been fixed.
3. RESI instructions that set lower-case names for residues did not work
properly in version 2016/4. Such names are now converted to upper case on
input so that they are compatible with other instructions.
4. If the wavelength is within 0.001 of 0.5136 it is recognized as
InKα. The following wavelengths were already recognized
(also within 0.001): 1.5418 CuKα, 1.3414 (GaKα),
0.7107 (MoKα) and 0.5609 (AgKα). This is reported
in the .cif file and f', f" and mu are set accordingly.
5. BOND $H now includes symmetry equivalent hydrogen atoms in the bond
lengths and angles tables, e.g. for a water molecule on a twofold axis.
6. The handling of symmetry equivalent atoms (referenced by _$N where N is
an integer) has been improved.
7. The 'recommended weighting scheme' suggested by the program now
defaults to
8. To improve the error diagnostics, atom names may not be used as RTAB
labels.
9. The .cif file should no longer contain symmetry equivalent bond
lengths, previously these could be present for bonds involving symmetry
equivalent atoms.
10. The maximum number of possible Q-peaks, set by the PLAN instruction,
has been increased from 999 to 3599.
11. The HTAB analysis of hydrogen bonds has been improved.
12. The 'lineprinter plots' (a relic from the distant past) have been
tidied up and should no longer contain any question marks.
Version 2016/4
1. A error involving the formatting of special position constraints
for certain space groups that caused the program to crash, introduced in
version 2016/3. has been fixed.
Version 2016/3
1. The residue numbers have been extended to allow the use of
one-character chain-IDs, e.g. A:1234 when used on the RESI instruction
and wherever residue numbers are used. The chain-ID may be an upper or
lower case letter, a digit or a space (default). There are thus 63
possible chain-IDs, compatible with PDB format. This only applies to
residue numbers, not classes, i.e. Z:JUNK is not allowed. The new program
PDB2INS written by Anna Lübben is able to convert PDB files to SHELXL
.ins files using this notation.
2. The transfer of CIF instructions from the end of the .hkl
file to the .cif file (see 2014/4 below) should now work
correctly.
3. Fixed atom coordinates are now output to the .cif file as
0.333333 and 0.666667 instead of 0.3333 and 0.6667 etc. This was only
necessary for CheckCIF, SHELXL uses the tolerance set by the SPEC
instruction to detect whether atoms are on special positions.
4. If no DISP instruction is provided and the wavelength is within
0.001 of: 1.5418 (CuKa), 1.3414 (GaKa), 0.7107 (MoKa), 0.5609 (AgKa)
or 0.5136 (InKa) the appropriate values of f', f" and mu are used for
the first 92 elements of the periodic table. If the wavelength is in
none of the above ranges and no DISP instruction is given, MoKa is now
assumed and a warning appears. Note that both shelXle and pdb2ins may
be used to generate DISP instructions for any wavelength, e.g. for
synchrotron data. It is important to use the correct values; for
example f' for Ni with CuKa radiation is -3, which could result in
nickel atoms being wrongly identified as manganese, and correct f"
values are required to determine the Flack parameter.
5. A number of error messages and warnings have been improved.
Version 2014/7
1. Several minor CIF format problems have been fixed.
2. At the start of the data_ segment in the .cif file written
by SHELXL-2014/7, the following two records appear:
_audit_creation_method 'SHELXL-2014/7'
_shelx_SHELXL_version_number '2014/7'
Programs processing the CIF file downstream from SHELXL may change
_audit_creation_method but they should NEVER CHANGE any CIF item
that begins with '_shelx_', because such CIF entries are reserved
for the SHELX programs. Recent CIFs on the Acta Cryst. C website
include several examples in which _shelxl_version_number has been
modified and usually made useless. Since it is possible that these
programs only treated items beginning with _shelx_ but not those
beginning with _shelxl_ as reserved, _shelxl_version_number has been
deprecated and replaced with _shelx_SHELXL_version_number.
3. To handle the case that other CIF processing programs
persist in corrupting the SHELXL version number, it is now also
included in the .res file as a remark (beginning with blanks
rather than REM so that it does not accumulate). It is then embedded
in the final .cif from SHELXL where it is 'checksum protected'!
I am grateful to Ton Spek for suggesting this elegant solution.
4. In the .cif file written by SHELXL, if the default
_diffrn_reflns_theta_full would be larger than
_diffrn_reflns_theta_max it is made equal to it. I have it on good
authority that CheckCIF will then no longer report it as an A alert.
5. The rejection criteria for the reflections used in the Parsons'
quotients have been modified slightly (suggested by Simon Parsons).
6. In the triangular table of bond lengths and angles in the
.lst file, angles that are not allowed according to the PART
rules should now be replaced by blanks.
Version 2014/6
1. Under certain circumstances involving previously merged data, a
corrupted .cif file could be produced. This has now been fixed.
Version 2014/5
1. It was possible for version 2014/4 to insert a superfluous ';' into the
.cif output file, with dire consequences. This has now been fixed
and the opportunity taken to tidy up some other items mainly affecting the
.cif file (see below).
2. The rarely used weighting factor e.sin(theta/lambda) was correctly
described in the .lst output file but not in the .cif file
and some of the documentation. It should now be consistent.
3. The use of EXYZ could cause some bonds to be missing in the .cif
file. They should now appear.
4. Torsion angles in the .cif file should now never appear with '_a'
tags etc. for different PARTs, unless ACTA TABS is set, and the PART rules
are now enforced more strictly for the torsion angles in the .cif
file generated using CONF.
5. ANIS C1 C3 > C6 was incorrectly also making C2 anisotropic, this has
now been fixed.
6. The linear absorption coefficient is now calculated and output to
the .lst and .cif files when NEUT is used to set neutron
scattering factors. Previously it was output as zero when NEUT but no
DISP was specified.
Version 2014/4
1. SHELXL and other programs read reflections from the .hkl file
until a reflection with h=0, k=0 and l=0 or a blank line is encountered.
This means that useful information that is specific to that .hkl
file may be added after this line. For example the end of such a file
produced by SADABS version 2014/4 was as follows:
0 -3 41 4.85301 3.01063 26
0 0 0 0.00 0.00 0
_exptl_absorpt_process_details 'SADABS 2014/4'
_exptl_absorpt_correction_type multiscan
_exptl_absorpt_correction_T_max 0.7489
_exptl_absorpt_correction_T_min 0.7208
_exptl_special_details
;
The following wavelength and cell were deduced by SADABS from the
direction cosines etc. They are given here for emergency use only:
CELL 0.71072 6.100 18.294 20.604 90.006 89.992 90.000
;
In this example, the cell following _exptl_special_details is not the same
as in the CELL used in the .ins file because there was a
reorientation matrix on the HKLF 4 instruction to transform the indices to
the conventional P2
2. Some HFIX or AFIX errors produced garbled error messages. They should
now be clearer.
3. At the request of users, if a TWIN matrix has a negative
determinant and is not -1 0 0 0 -1 0 0 0 -1, the twin fraction is no
longer reported as a Flack parameter. In such cases no Flack parameter
is now estimated.
4. The hydrogen positions should now be calculated correctly again for
AFIX 123 etc.
Version 2014/3
1. A serious bug in version 2014/2 affecting methyl groups (AFIX 33 etc.)
has been fixed.
Version 2014/2
1. The '_a' etc. tags are now only output to the .cif file if the
keyword 'TAGS' is present on the ACTA instruction (see 2014/1 below).
They are still output as before to the .lst file.
2. The handling of PARTs by AFIX, HFIX and HTAB has been improved and
several bugs fixed.
3. The nonsense error message that resulted when HFIX 33 or 37 is used for
an acetonitrile molecule has been made sensible. Because the CCN unit is
linear, geometric criteria cannot be used to place the hydrogens, but
HFIX 137 should work.
4. A bug in the implementation of the CONN instruction has been fixed.
5. WIGL may now be followed by the rms shift in position in Å (as
before) and then the rms percentage change in U or U
6. As stated for many years in the documentation, all six hydrogens in a
AFIX 12N group must have the same PART number; there are good technical
reasons for this. However it is now possible to start with HFIX/AFIX 123
etc., and then in the next job to split this into two AFIX 37 groups with
different PART numbers.
7.Although AFIX instructions were intended for placing hydrogen atoms, it
is also possible to use AFIX 30, 120 or 130 to set up ideal CF
DFIX 1.328 C1 F1 C1 F2 C1 F3
DFIX 2.125 F1 F2 F1 F3 F2 F3
SADI 0.1 C2 F1 C2 F2 C2 F3
Note the relatively soft SADI restraint to the next atom to allow the
CF
C2 ...
AFIX 9
C1 ...
AFIX 135
F1 3 0 0 0
F2 3 0 0 0
F3 3 0 0 0
AFIX 0
8. There is still some confusion about the use of SAME with RESI, which
was accentuated by a bug in the implementation. The bug has now been fixed.
SAME_XYZ, where XYZ is a residue name, now operates differently to SAME_N
(where N is a residue number) or SAME without a residue number, both of
which must be immediately followed by atoms in the same order as on the
SAME instruction (H atoms are ignored). SAME_XYZ no longer uses the
following atoms but is applied to all residues with the name XYZ, so the
atoms must have the same names in the same order in each of these
residues so that the program knows which are equivalent. For
example, if we have six THF solvent molecules which should be restrained
in this way, the THF molecules are preceded by 'RESI 1 THF', 'RESI 2 THF'
.. 'RESI 6 THF' and are each followed by RESI 0 (which can be omitted if
another RESI instruction follows immediately). In this case the THF atoms
should have the same names in the same order in each THF residue. Only
two SAME instruction are required and may (now) appear anywhere in the
.ins file:
SAME_THF O1 > C4
SAME_THF O1 C4 < C1
Hydrogen atoms can be added later with a single instruction:
HFIX_THF 23 C1 C2 C3 C4
Alternately 'SAME_1 O1 > C4' and 'SAME_1 O1 C4 < C1' could be
inserted before the first atom of each THF residue after the first,
that would be less elegant but would not require the same atom names to
be used in each THF residue. Since hydrogen atoms are ignored by SAME,
SADI not SAME should be used for H
SADI_WAT OW HW1 OW HW2
SADI_WAT HW1 HW2
or:
DFIX_WAT 0.84 OW HW1 OW HW2
DFIX_WAT 1.33 HW1 HW2
should work. These examples illustrate the way in which residues can be
used to make the .ins file much simpler and easier to
understand. Note however that because of a design limitation in
PLATON/CheckCIF, the number of characters in the atom name plus the
number of characters in the residue number (plus two if ACTA TABS is set)
should not be greater than 7.
Version 2014/1
1. In the .cif output file, '_a' has been added to all references to
PART 1 atoms, '_b' to PART 2 atoms etc., but not for atoms with negative
PART numbers. This prevents a deluge of A alerts when running CheckCIF
on structures in which atoms have the same names and residue numbers but
different PART numbers. This is allowed by the SHELXL and PDB
specifications, and is very convenient for applying the same restraints
to multiple conformations.
2. In the .pdb output file, element names have been added in
columns 77/78 and an END instructions has been added at the end for
compatibility with PYMOL.
3. A small error affecting the (equivalent) isotropic B-values
output to the .pdb file has been corrected.
4. HFIX should now work correctly with NEUT. However for deuterium atoms
it will still be necessary to change the atom names and scattering factor
numbers by hand.
5. '+filename' reads instructions from a file but does not copy them to
the .res file. This is useful for reading in long lists of standard
restraints. '++filename' also reads instructions from the named file
but copies them to the .res file where appropriate. Such include
files may call further files using '+filename' but not '++filename'.
'+filename' is echoed to the .res file if it is in the .ins
file but not if it is in a '+' or '++' file, '++filename' is never echoed.
6. XNPD with no parameters now defaults to +0.001 as stated in the
instructions.
7. CONF should now never create an empty loop in the .cif file,
which caused problems for some programs that read CIFs. Such loops could
arise because CONF now uses the central bond length and the angles as a
test to remove unwanted torsion angles.
8. Element names may now only appear once each on SFAC instructions.
However both H and D may be present and will result in special treatment
of H and D atoms (unless NEUT is specified before SFAC).
9. A bug has been fixed that could lead to HTAB instructions involving
symmetry equivalent atoms not being recognised.
10. Some minor improvements have been made to AFIX for generating
hydrogen atoms and a bug that sometimes prevented the generation of
PART n hydrogens attached to a PART 0 atom has been fixed.
11. CF
12. SAME_n plus atom names, where n is a residue number, is now allowed.
Note however that this will only make two residues equivalent; for a
structure containing e.g. many poorly defined THF solvent molecules,
a single SAME_THF plus atom names will make all the THF molecules
equivalent provided that they have the same atom names.
13. It should now no longer be possible for
_diffrn_reflns_Laue_measured_fraction_full in the .cif file to be
greater than 1.000.
Previously it could be slightly greater than 1.000 when the reflection
d-values for different twin components differed slightly (HKLF 5 format
or pseudo-merohedral twinning using a TWIN matrix).
14. The instruction 'RTAB D2CG atom1 atom2 ...' calculates the distance
(and its esd) of atom1 to the unweighted centroid of the remaining
atoms in the list.
15. If a non-standard space group is not recognized, i.e. its name
cannot be deduced from LATT and SYMM, the name is now given as ? rather
than '?' in the .cif file ('?' upset some CIF parsers).
16. 'BIND m n' where m and n are PART numbers allows atoms in PART m to
bond to atoms in PART n. This provides an addition to the usual PART rules
so that disorders inside disorders can be refined more easily. m and n may
be positive or negative.
17. If 'NOHKL' is present on an ACTA instruction, the .hkl and (if
relevant) .fab files are not included in the .cif file.
This is intended
for the intermediate stages of the refinement only; for deposition and
archiving it should not be used. This change was made under pressure from
some users against my better judgement; it is good science to deposit and
archive the original reflection data and the new facility may result in
these data being lost (accidentally or on purpose). The final .res
file is always included in the .cif file and can still be extracted
using shredcif.
18. If the twin factor refined with TWIN and BASF refines to a value
outside the range 0 to 1, F
Version 2013/4
1. A missing PART 0 instruction produced the rather misleading error
message "Cannot find .res file to insert it into .cif". The more useful
message "Bad AFIX 33 connectivity, C107_a bonds to no atoms" is now
output in the case in question. The program tries to find missing
AFIX 0 instructions but missing PART 0 instructions, which mess up the
connectivity table, are almost impossible to detect.
2. Setting the fourth L.S. parameter could cause the Flack parameter
to be determined too close to zero with a very small esd. To avoid
misuse, this has been fixed by allowing a maximum of only three L.S.
parameters.
3. The counting of the number of reflections for use in the .cif file
was not always accurate, primarily as a result of rounding errors
involving the resolution limits. This should now be more reliable.
4. For refinements against neutron data with the NEUT instruction, the
CHIV instruction can now be used as for X-ray data when an atoms makes
exactly three bonds to non-H/D atoms, in which case further bonds to H
or D are ignored. If an atom makes a total of exactly three bonds
including bonds to H or D, a CHIV instruction with the default value
of zero may be used to restrain planarity, e.g. for -NH-, -NH
Version 2013/3
1. If (for whatever reason) a Flack parameter defined by TWIN and BASF
refined to an appreciably negative value, this sometimes caused very
large 'Q peaks' as an indirect consequence of some calculated intensities
being negative. This has now been fixed but the value obtained from the
Parsons' quotients (without TWIN and BASF) should usually be quoted
anyway, see Parsons, Flack and Wagner, Acta Cryst. B69
(2013) 249-259.
2. A bug affecting the use of EADP in some complicated disordered
situations has been fixed.
3. CONF followed by explicit atom names should now no longer have
problems recognising atoms. CONF without atom names never had problems.
4. HTAB now follows the PART rules more closely.
5. It is now possible to use any combination of negative MORE, input
from a .fab file, and output to a .pdb file in the same run
(previously the same unit number was used for all three).
6. The space group Cmc21 is now reported correctly in the .cif file,
previously it was confused with Pmc21 when deducing the space group from
LATT+SYMM.
7. The heading for the table of "most disagreeable reflections" is now more
explicit.
8. The format used for reporting the weighting scheme in the .cif
file has been changed back to that used by SHELXL-97 for compatibility with
some local versions of the templates for making tables.
9. The refinement of two or more sets of hydrogen atoms with different PART
numbers attached to the same atom should now work correctly. Similarly
CH
Version 2013/2
1. The program should now no longer call itself a "beta-test".
2. References to shelxl_2012 in the .cif file have been changed to
shelxl_2013.
3. TWST 0 is now allowed and has been made the default. This causes all
twin components to be used for making the completeness and Friedel
coverage statistics. TWST 1 just uses the first component for this.
4. A small (<= 1 reflection) error in the calculation of
completeness and Friedel coverage has been corrected. No-one noticed.
Version 2013/1
1. A number of small bugs have been exterminated.
2. Multiple CPUs are now always used if available, there is no special
shelxl_mp version.
3. In view of the impressive data quality from the liquid
gallium anode, GaKα has been added to the standard radiations
recognised by the program (in addition to CuKα, MoKα and
AgKα).
Version 2018/2
1. If -T or -t are not used on the command line to specify the number
of threads to be used for parallel operation, it is set to the
maximum number available. Previously the number of threads
for the P1 expansion stage was set to 4 or less and the -t setting
was ignored for some operations.
2. The elements Am, Cm, Bk and Cf are now allowed for consistency with
SHELXL and CheckCIF.
3. The default values for -d and -e are now both 0.8. This makes the
program a little slower but improves the success rate.
4. The .res files written by SHELXT now contain BOND instead of
BOND $H.
5. The mean I/sigma(I) for systematic absences (where at least 10
of them were recorded) is now reported and space groups rejected for
which it is greater than 5.0.
6. The solutions are now sorted and only the best five saved. This
prevents the program from running out of file names after the first
26 and means that the solution with the file name *_a is more likely
to be the correct one.
Version 2014/5
1. The reflection list in the output .hkl is now terminated by a
reflection 0,0,0 as well as a blank line. All SHELX programs of the last
40 years accepted either as the end of the reflection list, but Olex2
did not.
2. A few minor changes have been made to the .lzt output
and to the command summary output when no filename is specified.
Version 2014/4 (first official release)
1. There is no longer an expiry date.
2. The program is highly parallel. It will use all available threads
unless
3. The structure found should now be optimally centred in the unit-cell.
4. The original TITL is converted to a REM, and a new TITL is generated
giving the filename and space group found by SHELXT. Further details of
the structure solution are given as REMs.
5. Some minor improvements have been made to the element assignment.
6. The listing file is now called .lxt to make it less likely to
be overwritten.
7. The ZERR instruction is now transformed as required if the axes had
to be redefined to get the conventional setting for the chosen space
group. None of the beta-testers reported this bug!
8. In response to suggestions by the beta-testers, ANIS and RIGU are no
longer inserted into the .res file.
9. In the .hkl files written by SHELXT, the last reflection is
followed by the blank line and CIF items carried over from the
original .hkl file, and then by:
_computing_structure_solution 'SHELXT 2014/4 (Sheldrick, 2014)'
Thus all these CIF items are automatically incorporated in the
.cif file written by SHELXL if it uses an .hkl file from
SHELXT.
Version 2014/4
1. When SHELXL embeds .hkl, .res or .fab files
into the .cif file, it replaces lines that begin with ';' and
are otherwise blank by lines that start with ')'. SHREDCIF now reverses
this and replaces ')' by ';' in otherwise blank lines.
2. The embedded .res file is retained in the shredded CIF file
because it is proving very useful for CheckCIF (and referees), but the
embedded .hkl and .fab files are stripped.
Version 2014/3
1. When SHREDCIF is run without a filename, it outputs its version
number followed by a brief description. To avoid confusing other
programs that might be calling SHREDCIF, when a filename is specified
the standard output is the same as for previous versions, provided
that there are no error messages, so it does not include the version
number.
2. The checksums may now appear anywhere in the same data_ segment
before or after the data to which they apply. Apparently some CIF
processing software has a habit of shuffling the CIF file!
3. The error diagnostics have been improved. For example, if a
checksum is given as '?' (presumably put there by a user who has
tried to 'improve' the CIF file), SHREDCIF now reports a bad checksum
and continues rather than reporting a corrupted CIF file and
terminating.
Version 2014/2
1. A bug has been fixed that caused the first line of each table heading
to be truncated. This was an indirect side-effect of change #1 in version
2014/1.
Version 2014/1
1. The formatting of the space group names has been improved in the RTF
output (for input to Microsoft Word or Open Office). No change is needed
to the ciftab.rta and ciftab.rtm template files.
Version 2013/2
1. The name following "data_" is now no longer converted to lower case
when two .cif files are combined.
1. The test data are now available on the download server as well as via
links on the homepage.
2. It is now possible to view the homepage and register from an iPhone.
I am very grateful to the following users for reporting bugs: Chris Anson,
John Bacsa, Andrei Batsanov, Christine Beevers, Paul Boyle, Bill Brennessel,
Bill Clegg, Fabio Dall'Antonia, Antonio DiPasquale,
Oleg Dolomanov, Alan Downward, Paul Emsley, Louis Farrugia, Jim Fettinger,
Stu Fisher, Tim Grüne, Ilia Guzei, Klaus Harms, Larry Henling,
Regine Herbst-Irmer, Julian Holstein, Håkon Hope, Jörg
Kärcher, Daniel Kratzert, Florian Kraus, Lennard Krause, Tony Linden,
Martin Lutz, Joel Mague, Curtis Moore,
Peter Müller, Bruce Noll, Marilyn Olmstead, Holger Ott, Sean Parkin,
Brian Patrick, Bob Pike, Tullio Pilati, Horst Puschmann, Kris Radaki,
Carmen Ramirez, Nigam Rath,
Joe Reibenspies, Frank Rominger, Amy Sarjeant, Thomas Schneider,
Ton Spek, Simon Teat, Jens Thomas,
Andrea Thorn, Karl Törnroos, Isabel Usón, Hubert Wadepohl,
Hilke Wolf, Christoph Wolper, Qingping Xu, Peter Zavalij, Matt Zeller,
Joe Ziller and many others.
I should particularly like to thank the following for their help with
the SHELX homepage: Lee Daniels, Tim Grüne, Regine
Herbst-Irmer, Julian Holstein, Christian Hübschle, Daniel Kratzert,
Peter Müller, Bruce Noll, Roland Pfoh and Andrea Thorn.