SHELX C/D/E: Difference between revisions

1,531 bytes added ,  5 November 2011
Line 86: Line 86:


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.
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.
=== how to prove that a molecular replacement solution is correct ===
From a [http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1111&L=CCP4BB&O=D&P=41977 November 2011 posting of George Sheldrick on CCP4BB]: We have unintentionally discovered a very simple way of telling whether
an MR solution is correct or not, provided that (as in this case) native
data have been measured to about 2.1A or better. This uses the current
beta-test of SHELXE that does autotracing (available on email request).
First rename the PDB file from MR to name.pda and generate a SHELX
format file name.hkl, e.g. using Tim Gruene's mtz2hkl, where 'name' may
be chosen freely but should be the same for both input files. Then run
SHELXE with a large number of autotracing cycles (here 50), e.g.
shelxe name.pda -a50 -s0.5 -y2
-s sets the solvent content and -y a resolution limit for generating
starting phases. If the .hkl file contains F rather than intensity the
-f switch is also required.
If the model is wrong the CC value for the trace will gradually
decrease as the model disintegrates. If the model is good the CC will
increase, and if it reaches 30% or better the structure is solved. In
cases with a poor but not entirely wrong starting fragment, the CC may
vary erratically for 10-30 cycles before it locks in to the correct
solution and the CC increases over three or four cycles to the value
for a solved structure (25 to 50%). The solution with the best CC is
written to name.pdb and its phases to name.phs for input to e.g. Coot.


== RIP with SHELXC/D/E ==
== RIP with SHELXC/D/E ==
1,330

edits