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I admit that made "impossible" more difficult to solve than "possible", but not in the way I had intended! Again, sorry about that. It is corrected now. The change in indexing arises because I am processing the simulated images with a default run of XDS and as you know the autoindexing picks an indexing convention at random. I flipped it back at the time, but when I just now went back to get the I(+)/I(-) I went just one step too far. Once again, sorry. It was not my intention to waste anyone's time! -James Holton MAD Scientist On 1/12/2013 2:09 PM, George Sheldrick wrote: > James, > > I had in fact just come to the conclusion that the indexing was > consistent with 3dko for 'possible' but not for 'impossible', > which I suppose was logical. > > George > >> 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 <tel:0031715274414> >>>> web: http://bsc.lic.leidenuniv.nl/people/skubak-0 >>> >> > > > -- > 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 >