SHELXE command line parameters
Experimental phasing with SHELXE
A typical SHELXE job for SAD, MAD, SIR or SIRAS phasing could be:
where xx.hkl contains native data and
xx_fa.hkl, which should have been created by SHELXC or
XPREP, contains F
Normally the heavy atom enantiomorph is not known, so SHELXE
should also be run with the
NCS may now also 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 then 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 -n command line switch is not required.
If the heavy atoms are present in the native structure (e.g.
for sulfur-SAD but not SIRAS for an iodide soak)
If -x is specified and a PDB-format reference file name.ent is provided, the origin shift and mean phase errors are calculated 'on the fly'. 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. This is a quick way of checking whether the substructure is correct, but note that it may be necessary to invert it with -i
Expanding and verifying a MR solution with SHELXE
To start from a MR model without other phase information, the PDB file from MR should be renamed (to xx.pda to match the xx.hkl native data file) and input to SHELXE, e.g.
The number of tracing cycles is usually more than for experimental phasing to reduce model bias. If the MR model is large but does not fit well, -o should be included to prune it before density modification by eliminating individual residues to optimize the CC for the model against the native data. For large structures, this optimization may be restricted to groups of two or more residues to fit into the available computer memory; the -u switch may be used to fine-tune the memory allocation for this.
Tracing from an MR model requires a favorable combination of model quality, solvent content and data resolution. However, if the CC against the native data exceeds 25% after several cycles of autotracing, it is almost certain that the structure is solved! It is necessary to do several cycles to reduce model bias, the CC after the first cycle may be artificially high.
MRSAD - combining MR and experimental phasing
If both a MR model and anomalous data are available, but neither are good enough to give a good model on their own, the two approaches may be combined. To solve a structure in this way with MRSAD, first SHELXC must be used to generate the file xx_fa.hkl as for experimental phasing, then:
This uses phases from the MR model to generate the heavy atom substructure, which can be optimized with -z as with experimental phasing. The substructure is then used to derive SAD phases that are combined with the phases from the MR model. The -o, -z and -h flags are often needed for this mode. This approach ensures the the heavy-atom substructure refers to the same choice of unit-cell origin as the MR fragment.
Using phases from other sources
If approximate phases are available, SHELXE may be used to refine them and make a poly-Ala trace:
where zzz is phi (phs file format), fcf (SHELXL LIST 6 format) or hlc (Hendrickson-Lattman coefficients, e.g. from SHARP or BP3). However it is recommended that if heavy atoms are found by SHELXD, they should be input directly into SHELXE with the -z switch to refine them before phasing, rather than using some other program to derive phases from the heavy atoms and input these phases to SHELXE. Reading in the heavy atoms has several advantages, for example they are used to make a 'no-go map' so that SHELXE does not trace the main-chain through them!
SHELXE output files
In all cases, native data are read from
xx.hkl in SHELX format, and the final phases are output
to xx.phs (or xx_i.phs if
Alphabetical list of SHELXE options (defaults