Ok, I'll bite. "I dare anyone who considers themself an expert macromolecular crystallographer to find a way to build out of this map."
I put emphasis on "this map". "Short of actually cheating (see below), there doesn't seem to be any automated way to arrive at a solved structure from these phases" I put emphasis on "these phases". I think the real challenge (and one that makes for an excellent macromolecular crystallographer) is how well one can interpret a map with poor phases. That being said, I think a recalculation of the map using any other information besides the map itself should not be allowed. PS. I'd like to see what the pre-DM phases look like. There's a huge chunk of the protein that is completely flattened out in impossible.mtz . F On Jan 12, 2013, at 1:50 PM, James Holton <jmhol...@lbl.gov> wrote: > > Woops! sorry folks. I made a mistake with the I(+)/I(-) entry. They had > the wrong axis convention relative to 3dko and the F in the same file. Sorry > about that. > > The files on the website now should be right. > http://bl831.als.lbl.gov/~jamesh/challenge/possible.mtz > http://bl831.als.lbl.gov/~jamesh/challenge/impossible.mtz > > md5 sums: > c4bdb32a08c884884229e8080228d166 impossible.mtz > caf05437132841b595be1c0dc1151123 possible.mtz > > -James Holton > MAD Scientist > > On 1/12/2013 8:25 AM, James Holton wrote: >> >> Fair enough! >> >> I have just now added DANO and I(+)/I(-) to the files. I'll be very >> interested to see what you can come up with! For the record, the phases >> therein came from running mlphare with default parameters but exactly the >> correct heavy-atom constellation (all the sulfur atoms in 3dko), and then >> running dm with default parameters. >> >> Yes, there are other ways to run mlphare and dm that give better phases, but >> I was only able to determine those parameters by "cheating" (comparing the >> resulting map to the right answer), so I don't think it is "fair" to use >> those maps. >> >> I have had a few questions about what is "cheating" and what is not >> cheating. I don't have a problem with the use of sequence information >> because that actually is something that you realistically would know about >> your protein when you sat down to collect data. The sequence of this >> molecule is that of 3dko: >> http://bl831.als.lbl.gov/~jamesh/challenge/seq.pir >> >> I also don't have a problem with anyone actually using an automation >> program to _help_ them solve the "impossible" dataset as long as they can >> explain what they did. Simply putting the above sequence into BALBES would, >> of course, be cheating! I suppose one could try eliminating 3dko and its >> "homologs" from the BALBES search, but that, in and of itself, is perhaps >> relevant to the challenge: "what is the most distance homolog that still >> allows you to solve the structure?". That, I think, is also a stringent >> test of model-building skill. >> >> I have already tried ARP/wARP, phenix.autobuild and buccaneer/refmac. >> With default parameters, all of these programs fail on both the "possible" >> and "impossible" datasets. It was only with some substantial tweaking that >> I found a way to get phenix.autobuild to crack the "possible" dataset (using >> 20 models in parallel). I have not yet found a way to get any automation >> program to build its way out of the "impossible" dataset. Personally, I >> think that the breakthrough might be something like what Tom Terwilliger >> mentioned. If you build a good enough starting set of atoms, then I think >> an automation program should be able to take you the rest of the way. If >> that is the case, then it means people like Tom who develop such programs >> for us might be able to use that insight to improve the software, and that >> is something that will benefit all of us. >> >> Or, it is entirely possible that I'm just not running the current software >> properly! If so, I'd love it if someone who knows better (such as their >> developers) could enlighten me. >> >> -James Holton >> MAD Scientist >> >> On 1/12/2013 3:07 AM, Pavol Skubak wrote: >>> >>> Dear James, >>> >>> your challenge in its current form ignores an important source >>> of information for model building that is available for your >>> simulated data - namely, it does not allow to use anomalous >>> phase information in the model building. In difficult cases on >>> the edge of success such as this one, this typically makes >>> the difference between building and not building. >>> >>> If you can make the F+/F- and Se substructure available, we >>> can test whether this is the case indeed. However, while I >>> expect this would push the challenge further significantly, >>> most likely you would be able to decrease the Se incorporation >>> of your simulated data further to such levels that the anomalous >>> signal is again no longer sufficient to build the structure. And >>> most likely, there would again exist an edge where a small >>> decrease in the Se incorporation would lead from a model built >>> to no model built. >>> >>> Best regards, >>> >>> -- >>> Pavol Skubak >>> Biophysical Structural Chemistry >>> Gorleaus Laboratories >>> Einsteinweg 55 >>> Leiden University >>> LEIDEN 2333CC >>> the Netherlands >>> tel: 0031715274414 >>> web: http://bsc.lic.leidenuniv.nl/people/skubak-0 >> >
