Most likely result is that sites are wrong?

But check your correation coefficients between the anom signals from the two data sets - maybe there is no real signal past a low resolution cut off?
  Eleanor

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Hi: I am using Ccp4i (v 6.01) and started with a pair of SAD datasets (.sca files from denzo) and then ran the shelxc/d/e suite with them. I got some probably mediocre hits (cc<12%) but decided to use the best atoms from the shelx hits and refine 'em with mlphare -- the sca file I described I ran through scalepack,truncate and cad to get the mtz file to refine against the shelx sites. I have made sure I'm refining anom.occupancy only (Se atoms) but I find the sites and their occupancy are being consistently refined to 0, often within ~8 cycles. Any ideas what I may be doing wrong?

Thanks for your help

Alex



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