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SHELX C/D/E: Difference between revisions
→The free lunch algorithm (FLA): beta-test notes
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The new switch -e may be used to extrapolate the data to the specified resolution (the '''''free lunch algorithm'''''), based closely on work by the Bari group (Caliandro ''et al''., ''Acta Crystallogr''. (2005) '''D61''', 556-565) and independently implemented in the program [[Acorn]] (Yao ''et al''., (2005) ''Acta Crystallogr''. '''D61''', 1465-1475): -e1.0 can produce spectacular results when applied to data collected to 1.6 to 2.0 Å, but since a large number of cycles is required (-m400) and the 'contrast' and 'connectivity' become unreliable (the pseudo-free CC is the only reliable map quality indicator when the FLA is used), it may be best to establish the substructure enantiomorph and solvent content without -e first. The default setting when -e is not specified is to fill in missing low and medium resolution data but not to extrapolate to higher resolution than actually measured (to switch off this filling in, use -e999). The resolution requirements for the FLA still need to be explored, but so far there have been no reports of it causing a deterioration in map quality, and in a few cases the mean phase error was reduced by as much as 30º relative to density modification without it.<br> | The new switch -e may be used to extrapolate the data to the specified resolution (the '''''free lunch algorithm'''''), based closely on work by the Bari group (Caliandro ''et al''., ''Acta Crystallogr''. (2005) '''D61''', 556-565) and independently implemented in the program [[Acorn]] (Yao ''et al''., (2005) ''Acta Crystallogr''. '''D61''', 1465-1475): -e1.0 can produce spectacular results when applied to data collected to 1.6 to 2.0 Å, but since a large number of cycles is required (-m400) and the 'contrast' and 'connectivity' become unreliable (the pseudo-free CC is the only reliable map quality indicator when the FLA is used), it may be best to establish the substructure enantiomorph and solvent content without -e first. The default setting when -e is not specified is to fill in missing low and medium resolution data but not to extrapolate to higher resolution than actually measured (to switch off this filling in, use -e999). The resolution requirements for the FLA still need to be explored, but so far there have been no reports of it causing a deterioration in map quality, and in a few cases the mean phase error was reduced by as much as 30º relative to density modification without it.<br> | ||
=== notes about the beta-test SHELXE === | |||
There is a beta-test version of SHELXE available upon request from George Sheldrick. | |||
Among other features and improvements, this version does autotracing: a poly-Ala trace will be written to the output .pdb file. In general the structure is solved if the CC for the trace is over 25% or the ratio of residues traced to the number of chains is greater than about 10. | |||
For this version, the -a option sets the number of global autotracing cycles; -a on its own is equivalent to -a3. | |||
== RIP with SHELXC/D/E == | == RIP with SHELXC/D/E == | ||