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I'm not sure about question (1), but here are some other ideas:
On Fri, Oct 26, 2012 at 12:19 PM, Heather Condurso
2. Is it likely that I will find a solution with the anomalous signal only going to 4.0A? Are there other parameters that may clue me in as to whether or not it may be possible with this data? My data is also anisotropic. Does that play a role in finding a solution? I have other data sets, but in those the mosaicity varies outside the ideal range. In this set the mosaicity varies between 0.2 and 0.5 when I integrate the images without fixing the mosaicity.
I don't think this resolution cutoff is necessarily a problem if the sites are ordered; people have certainly solved SeMet structures with worse, and it's more important to have high enough resolution overall that you can get an interpretable map. Anisotropy (how much?) is more likely to be a problem but Phaser at least can correct for this later. As far as mosaicity is concerned, the intensities are likely to be noisier, but if you have complete, redundant data you may still be able to find sites. One thing to keep in mind: you don't need to find all of the sites immediately, in fact it is better to aim a little lower because wrong sites are worse than missing sites. (Some of course may be disordered anyway.) Once you get to the phasing step the rest of the substructure will be filled in based on initial phases; it's an iterative process. I would try searching for 18 sites (approximately).
3. I've also tried to use the full search, but I'm not sure if it is working or not. I am using the GUI with version 1.7.3-928 on a Mac running OS 10.6.8. I just realized now that this is not the latest version and I can try it on another machine that I know is running 1.8.1-1168. None the less, the run status window only shows that it is running, but the log display only shows the initial search parameters, not what it is currently doing. I also tried using different rescoring and the log display is blank. Does this mean it isn't doing anything? Or should I be more patient? Some of these have been running for days....
I don't think HySS should take days to run... could be a bug, or could be a fatal crash (the GUI won't notice these and will assume the program is just taking a long time). I would definitely recommend updating, not least because there have been quite a few improvements to Phaser (and the GUI, for that matter). If you've stumbled across a bug in HySS we'd want to make sure it isn't already fixed in a newer version. A more general question: have you tried just running AutoSol yet? It will handle many of these issues automatically, and is relatively fast and very easy to set up. It will automatically try to build a model too, which is going to be the most reliable way of telling whether the phases are correct or not. -Nat