Shelxl-97 Program For Crystal Structure Refinement
The improvements in the program SHELXL have been closely coupled with the development and increasing importance of the (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the.hkl and.ins files required for further with SHELXL.
Recent developments in SHELXL facilitate against neutron diffraction data, the treatment of H atoms, the determination of the input of partial structure factors and the of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors. Introduction The first version of SHELX dates back to about 1970 and, after extensive testing, it was first released in 1976. Since then the program system has been developed continuously. The early history has been described by Sheldrick (2008). The present paper is intended to explain the philosophical and crystallographic background to developments between 2008 and 2015 in SHELXL, the program in the SHELX system responsible for Although SHELXL may also be used for the of macromolecular structures against high-resolution data, most of the new developments have concentrated on the of chemical structures, such as those published in Section C of Acta Crystallographica. Readers not familiar with SHELX may find it useful to look at Sheldrick (2008) before reading this paper.
A major change since 2008 is that the distribution is performed via the SHELX homepage ( ), which also provides a great deal of documentation, tutorials and other useful information. The programs are updated more frequently than in the past and the list of recent changes should be consulted regularly to see if it is necessary to download a new version. The homepage also contains a list of registered users (but not their email addresses); currently there are over 8000 spread over more than 80 countries.
New Journal of Chemistry S4. (SHELXL 97, 2012).1 The refinement of non-hydrogen atoms was done with. SHELXL-97, Program for X-ray Crystal Structure Refinement. Full-text (PDF) The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the.
Crystal Structure
SHELX workshops are announced on the homepage, and many of the talks given at these workshops may be downloaded there. SHELXL is compiled with the Intel ifort FORTRAN compiler using the statically linked MKL library, and is available free to academics for the 32- or 64-bit Windows, 32- or 64-bit Linux and 64-bit Mac OS X operating systems. Multithreading is achieved using OpenMP along the lines suggested by Diederichs (2000), and the program is particularly suitable for multiple-core processors. Archiving crystallographic data To make the deposition and archiving of reflection data as simple as possible, the written by SHELXL now includes the.hkl reflection data file, embedded as text: shelxhklfile.
Reflection data in SHELX HKLF 2, 3, 4 or 5 format.; shelxhklchecksum 12345 The checksum provides a check that the data have not been corrupted accidentally. The.res results file from the and the.fab file (see below), if used in the are embedded into the in the same way.
The SHELX program SHREDCIF may be used to extract these files from the archive and rename the.res file to.ins, for example to perform further refinements with SHELXL. The intention is that such CIFs containing embedded data should become standard for deposition and archiving. It is particularly convenient that only one file is needed. Identifiers beginning with shelx are reserved for use by the SHELX programs, but of course other program authors may use a similar construction for embedding the reflection data etc.
Users who do not wish to preserve their carefully measured data for posterity in this way have criticized the embedding of the reflection data on the grounds that ( a) the resulting is too large for submission with a paper for publication and that ( b) certain CIF-processing programs take a long time to read such a and may even choke in the attempt. However, it should be noted that ( a) the figures submitted with a paper often involve larger files and ( b) SHREDCIF can usually read and dismember such a in less than one second! To generate a without intensity data for other purposes, e.g. For input to a molecular graphics program, the keyword NOHKL may be used in the SHELXL ACTA instruction.
It is difficult to understand why several leading chemical journals still only require the deposition of the atom coordinates, etc., but not the reflection data, especially now that the Cambridge Structural Database (CSD; Allen, 2002) accepts the new CIFs and strongly encourages deposition of the reflection data. A simple solution would be for journals to require a confirmation that the full data have been deposited with the CSD (Bruno & Groom, 2014) or COD (Gražulis et al., 2012), analogous to the way in which the PDB requires deposition of the structural and reflection data before issuing a PDB ID. Including items at the end of the.hkl file Since SHELX76, the reflection data have been read until a reflection with indices 0,0,0 or a blank line (or card) or the end of the file was encountered. The rest of the file was never read by the SHELX programs.
This means that additional data specific to that data set, such as details of the data collection and processing, may conveniently be appended to the.hkl file, which is a much safer way of preserving them than putting them in a separate file. For example, the Bruker scaling program SADABS (Krause et al., 2015) now appends format items such as those shown below to the.hkl file that it outputs: exptlabsorptprocessdetails `SADABS 2014/4' exptlabsorptcorrectiontype multi-scan exptlabsorptcorrectionTmax 0.7489 exptlabsorptcorrectionTmin 0.7208 exptlspecialdetails; The following wavelength and cell were deduced by SADABS from the direction cosines etc.
Acta Crystallographica Section C-crystal Structure Communications
They are given here for emergency use only: CELL 0.71072 6.100 18.294 20.604 90.006 89.992 90.000; SHELXL uses the items found at the end of the.hkl file to replace items to which it would otherwise have given the value `?' It ignores all other items. So in this example, the first four items find their way (left justified) into the output but although exptlspecialdetails is legal for a it is not included as a item because this identifier would not otherwise have been output. However, it is still included in the.cif file as part of the embedded.hkl file, so that the information is not lost. Unfortunately, because of a fundamental design weakness (the same character `;' is used for both the beginning and end of a text item; it would have been better to have used a different terminator such as `:'), SHELXL has to replace `;' in this example by `)' when embedding the.hkl file, and SHREDCIF repairs the damage by turning a leading `)' in an otherwise blank line back to `;'. In this example, the cell following exptlspecialdetails is not the same as in the CELL instruction used in the.ins file, because there is a reorientation matrix in the HKLF 4 instruction to transform the indices to the conventional P2 12 12 setting for the However, it is still useful to preserve it in case the.hkl file becomes orphaned.
Against neutron diffraction data and special facilities for H atoms The new features in SHELXL for against neutron data have been discussed recently by Gruene et al. If a NEUT instruction is placed before SFAC, neutron scattering factors are employed, and the default bond lengths to H or D atoms are lengthened to correspond to internuclear distances rather than the distances appropriate for against X-ray data. Whereas for X-rays H and D are treated specially, for neutrons they are treated as normal atoms. The HFIX and AFIX instructions may still be used to generate starting positions for H and D atoms, but it is recommended to use geometric restraints rather than a riding model for their against neutron data. This is particularly important when anti-bumping restraints are applied; they work much better for a restrained than for a riding-model of the H and D atoms against neutron data. Chiral volume restraints for against neutron data The chiral volume restraint CHIV, which is often used for macromolecular is interpreted as follows if NEUT is set.
If three atoms other than H or D are bonded to the atom in question, the H and D atoms are ignored and the CHIV restraint operates in the same way as for a against X-ray data. If there are exactly three bonded atoms including H and D, the latter are used in the restraint. Thus, CHIV 0 N1 could be used to restrain a terminal –NH 2 group to be planar, and CHIV with a nonzero target value could be used to make it nonplanar. Other new facilities for H atoms and CF 3 groups Except where the NEUT instruction is used, both H and D are now treated as special in the input syntax. This is useful when both are present, e.g. When the crystals came from an NMR tube containing a deuterated solvent.
The AFIX instructions for CH 3 groups may now also be used to set up CF 3 groups, but it is better to refine these as rigid groups or with distance restraints ( DFIX or SADI) than by applying a riding model, because the latter can be unstable. An HTAB instruction without any parameters instructs the program to find possible hydrogen bonds. These now include C—H⋯O interactions when the C atom is directly or indirectly attached to an electronegative atom (Taylor & Kennard, 1982). Such weak interactions involving H atoms attached to peptide C α atoms are common in protein structures (Desiraju & Steiner, 1999). The resulting full HTAB and EQIV instructions are appended after the END instruction of the.res file and need to be (selectively) transferred to the beginning of the.ins file, so that they will be included in the generated by the next This facilitates the generation of tables of hydrogen bonds, and helps to prevent hydrogen bonds involving symmetry-equivalent atoms from being overlooked. Estimates of standard uncertainties One side effect of the inclusion of Friedel opposites is that there will be nearly twice as many data for the of a noncentrosymmetric structure, which, using the usual least-squares algebra, would lead to a reduction in the estimated standard uncertainties of all parameters by a factor of nearly 2 1/2.
SHELXL now uses the number of unique reflections as defined by the Laue group, rather than the number of observations, in the formula used to estimate the standard uncertainties (Spek, 2012). It could be argued that all reflection intensities are independent measurements, and this was approximately true for unscaled data from point detectors before the introduction of focusing optics. However, it is now standard practice to scale the data so that equivalent reflections (usually including Friedel opposites) become more equal, in order to correct for absorption and differences in the effective crystal volume irradiated, and then the equivalent reflections can no longer be regarded as independent observations. In some cases, this change may result in a modest increase in the estimated standard uncertainties, but these were generally underestimated anyway (Taylor & Kennard, 1986). The new method of estimating standard uncertainties also applies to twinned structures, where some SHELXL97 users were required by referees to throw away some of their carefully measured data so that the number of observations would be equal to the number of unique reflections.
Now all the experimental data may be used and the estimated standard uncertainties should be more realistic. With SHELXL97, it was necessary to use the third least-squares parameter to correct the estimated standard uncertainties; this is not required anymore (except for `SQUEEZEd' structures). Input of partial structure factors The new ABIN instruction was primarily designed to facilitate the use of the SQUEEZE facility (Spek, 2015) in the program PLATON (Spek, 2009), but it can also be used to input a bulk solvent model for a macromolecule. PLATON calculates the partial structure factors corresponding to a blob of unmodelled difference density and writes them to the.fab file. The ABIN instruction causes h, k, l, A and B to be read from the.fab file, where A and B are the real and imaginary components, respectively, of a partial These reflections are read in free format (one reflection per line) and may be in any order.
Duplicates, and reflections outside the resolution limits for are ignored. Symmetry equivalents are generated automatically. At least one symmetry equivalent (according to the point group) of each reflection present in the.hkl file, including all reflections in all twin components if the structure is twinned, should be present in the.fab file. For twinned structures, it is necessary first to use the new LIST 8 instruction (see below) to generate detwinned data for input to PLATON. The A and B values refer to the untwinned structure, but in the case of a twinned structure, after applying the appropriate symmetry transformations, they are added to the calculated structure factors for all twin components. ABIN takes two free variable numbers (Sheldrick, 2008) n 1 and n 2 as parameters.
The A and B values read from the.fab file are multiplied by kexp−8 π 2 Usin 2 θ/ λ 2, where k is the value of free variable n 1 and U is the value of free variable n 2. These two optional parameters may be needed when the partial structure factors come from a bulk solvent model of a macromolecule, but are probably not needed for use with SQUEEZE. SQUEEZE should only be used where it is not possible to model the disordered solvent by normal methods, e.g. When there is a continuous ribbon of diffuse difference density along one of the unit-cell axes. Partial structure factors and ABIN should always be used in preference to the old procedure of modifying the input.hkl file, which made it impossible to remodel the disordered density should a better method become available. Extending the PART number concept The use of PART numbers, introduced in SHELXL93, has proved invaluable in the of disordered structures. Two atoms are considered to be bonded if they have the same PART number or if one of them is in PART 0.
The resulting connectivity table is used for the generation of H atoms ( HFIX and AFIX), for setting up restraints such as DELU, SIMU, RIGU, CHIV, BUMP and SAME, and for generating tables of geometric parameters ( BOND, CONF, HTAB). Usually, most of the atoms are in PART 0, but, for example, a molecule or side chain disordered over three positions could use PART 1, PART 2 and PART 3. If the PART number is negative, bonds are not generated to symmetry-equivalent atoms. It should be noted that positive PART numbers 1, 2, 3 etc. Correspond to the alternative location indicators A, B, C etc. In PDB format. However, this notation is difficult to use when there is a disorder within a disorder.
A BIND instruction that specifies two numbers may now be used to get around this problem. For example, BIND 2 4 means that, in addition to the usual PART rules, atoms in PART 2 may also bond to atoms in PART 4. Negative PART numbers are allowed in the BIND instruction. As an example, consider an n-butyl substituent coordinated through atom C1 that splits into two disorder components at C2.
Atom C1 is then in PART 0, C2 A, C3 A and C4 A in PART 1, and C2 B, C3 B and C4 B in PART 2. Atom C1 is bonded to both C2 A and C2 B but, because these two atoms have different PART numbers, H atoms will be generated correctly using the HFIX instruction. However, if there is a further disorder starting at atom C3 B, this cannot be handled easily by SHELX97. Atoms C3 B and C4 B can be split into C3 B′ and C4 B′ in PART 3 and into C3 B′′ and C4 B′′ in PART 4, but then atoms C3 B′ and C3 B′′ are not bonded to C2 B.