You can check for consistent indexing using the program Pointless. The more recent versions (from version 1.5.0, perhaps best obtained from ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/) can use a PDB file as the reference (calculating structure factors from coordinates)
Phil On 10 Aug 2010, at 06:58, George M. Sheldrick wrote: > > There are two different but equally good ways of indexing the reflections > in space group I213, so there is a 50% chance that your new solution and > the refined structure will be indexed differently, in which case the > phases will not agree. Also you can easily improve the experimental phases > from shelxe by using the beta-test version that does iterative main-chain > tracing (available by sending me an email while I am still developing it). > > George > > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 > > > On Mon, 9 Aug 2010, wtempel wrote: > >> Dear colleagues, >> >> here is one cunning plan: >> >> to quickly evaluate the anomalous signal of a test data set with a >> non-interactive script that: >> 1. solves the structure using SAD >> 2. does some solvent flattening >> 3. compares the resulting phases against calculated phases from a >> refined, isomorphous structure. Generates some "global" measure of >> phase error (deviation from refined, calculated phases). >> >> Not very original, but still failing in my hands. >> >> 1., 2. (shelxc/d/e) - check. >> 3. a) take model amplitudes, phases and weights (F, PHIC, FOM(C)) from >> a refmac MTZ file - check. >> 3. b) cad PHI, FOM from the shelxe output with the selected columns >> from the refmac MTZ - check. >> 3. c) display reasonable maps using either of F-PHIC-FOM(C) or >> F-PHI-FOM combinations - check. >> 3. d) >> >> cphasematch -mtzin cad_ori.mtz -mtzout phasematch.mtz \ >> -colin-fo "/*/*/[F,SIGF]" -colin-phifom-1 "/*/*/[PHIC,FOM]" \ >> -colin-phifom-2 "/*/*/[PHI_ori,FOM_ori]" >> >> Now, I did expect to see a reasonable map using the F- >> phasematch.Phi_fom.phi-phasematch.Phi_fom.fom combination that would >> resemble F-PHI-FOM, but superimposed onto F-PHIC-FOM(C). But the F- >> phasematch.Phi_fom.phi-phasematch.Phi_fom.fom map does not resemble >> the protein structure at all. >> >> It is slowly coming to me that I must be doing this the wrong way. Can >> anyone spot the problem? By the way, the crystal is cubic insulin >> (a=78 A.) I would be happy to send out the data, the phasematch.mtz is >> just 140 kB in size. >> >> Many thanks, >> Wolfram Tempel >> >>
