SHELX C/D/E: Difference between revisions

SHELX C/D/E (edit)

Revision as of 15:20, 5 March 2014

1,051 bytes removed , 5 March 2014

RIP

Kay

Bureaucrats

1,328

edits

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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>
-=== notes about the beta-test version of SHELXE ===
+=== RIP ===
-There is a beta-test version of SHELXE available upon request from George Sheldrick.
+SHELXE inserts HKLF 4 and END before the first negative peak when writing the revised substructure to the .hat file. Normally this is a good way of finding where the noise begins, but for RIP if you want to recycle the negative peaks these lines should be removed.
-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.
-Use with [[hkl2map]]: let hkl2map find which enantiomorph is probably correct and then run a final SHELXE job from the command line, using the options -a3, -q (unless it is known that there are no helices) and (if the resolution is 2A or better) -e1.0 (or highest resolution -0.8, if more).
-NCS can be taken into account by adding the -n option.
-Use for RIP: the beta-test SHELXE inserts HKLF 4 and END before the first negative peak when writing the revised substructure to the .hat file. Normally this is a good way of finding where the noise begins, but for RIP if you want to recycle the negative peaks these lines should be removed.
-Nice writeup from GMS, as of Jan 13, 2013: is at [https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1301&L=ccp4bb&F=&S=&X=160F8F2598F868FF2A&P=83871].
 === how to find out if a molecular replacement solution is correct or wrong ===