SHELX C/D/E: Difference between revisions

   

'''SHELXC''' is designed to provide a simple and fast way of setting up the files for the programs '''SHELXD''' (heavy atom location) and '''SHELXE''' (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. These three programs may be run in batch mode or called from a GUI such as [[CCP4i]] or (better) [[hkl2map]]. SHELXC is much less versatile than the Bruker AXS XPREP program for this purpose, but if you are sure of the space group and there are no problems with the indexing or twinning and the f’ and f” parts of the scattering factors do not need to be refined, SHELXC should be adequate. SHELXC can read either HKL2000 format .sca files or SHELX .hkl files (F-squared unless the -f switch is used to specify F). To transfer data from CCP4 it is advisable to generate .sca files using 'output unmerged polish' from SCALA or to use the program mtz2sca written by Tim Grüne and supplied with SHELX.  The current version of SHELXC outputs extra useful diagnostic statistics if fed unmerged data. SHELXC, SHELXD and SHELXE are stand-alone executables that do not require environment variables or parameter files etc., so all that is needed to install them is to put them in a directory that is in the ‘path’ (e.g. /usr/local/bin or ~/bin under Linux).

<p>The above command line could be used under UNIX or Windows; under UNIX the commands to run SHELXC, SHELXD and SHELXE and the instructions for SHELXC may also be combined into a single script file as shown in the following examples. In these scripts, the instructions start on the line after '<<EOF' and are terminated by 'EOF'. The instructions may be given in any order; CELL (unit-cell), SPAG (space group in PDB notation, spaces are ignored) and FIND (followed by the number of heavy atoms) must be given; the optional instructions SFAC, MIND, NTRY, SHEL, ESEL and DSUL, if present, are copied to the SHELXD input file. <br><br>

In general the critical parameters for locating heavy atoms with SHELXD are:

RIP (without using anomalous scattering) or RIPAS (like SIRAS, assuming that the anomalous atoms are also those most sensitive to radiation damage) can be capable of solving difficult structures. A typical procedure on a third generation synchrotron beamline is to collect the 'before' dataset with an attenuator in the beam, then to fry the crystal for a couple of minutes with the unattenuated beam, and finally to collect an 'after' dataset with the attenuator in. In the SHELXC instructions, the 'before' data are called 'NAT' or 'BEFORE' and the 'after' data are called 'RIP' or 'AFTER'. The critical parameter is the scale factor applied to the 'after' data after both datasets have been brought onto a common scale. This is set by the SHELXC instruction 'DSCA' and should usually be in the range 0.95 to 1.00. This scale factor may also be used for SIR and SIRAS, where it is applied to the native data, but it appears to be less critical than for RIP. For RIPAS, the 'after' data should be called 'RIPA' and the 'RIPW' instruction specifies the weight w (default 0.6) for the anomalous contribution from the 'before' dataset (a weight 1–w is applied to the 'after' data).

In RIP or RIPAS phase determination is usually necessary to recycle the 'heavy atom' sites by renaming the output .hat (or _i.hat) file as .res and rerunning SHELXE. It is advisable to edit this file so as to retain the stronger negative sites, these may well correspond to the new positions of displaced atoms. SHELXE can read negative occupancies but SHELXD can only search for positive atoms. It should be noted that in a pure RIP experiment, both hands of the radiation damage substructure will give the same figures of merit, but one will lead to an electron density map that is a mirror image of the true map (the helices will go the wrong way round). <br>