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SHELX C/D/E: Difference between revisions
→notes about the beta-test version of SHELXE
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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 == | ||