Santosh,
Although I appreciate your ingenuity and I agree that SIRAS is an
excellent idea in the real world if you have only partial Se occupancy,
I'm afraid I think it is "cheating" to use more than one of the
challenge datasets at a time. The scenario I wanted to test is the
all-too-common "we only had that one good crystal" situation.
Then again, I do think it is interesting to ask how low the Se
incorporation can go before SIRAS fails. Even if it is under the
idyllic "perfect isomorphism" situation here. I have now put up 1%
increments between frac0.90.mtz and frac1.00.mtz. Do you think
you/Autorickshaw can solve it with frac0.99.mtz vs frac0.1.00.mtz ?
If you'd like to test in the presence of non-isomorphism, I'd recommend
using the "radiation damaged" simulated dataset here:
http://bl831.als.lbl.gov/~jamesh/workshop2/decaying.mtz
as the derivative. It is about 18% different from frac0.00.mtz (100%
Se, but badly decayed).
Thanks for all the great ideas!
-James Holton
MAD Scientist
On 1/15/2013 2:06 AM, Santosh Panjikar wrote:
> Hi James,
> The datasets frac.80.mtz to frac.100.mtz are challenging to solve using SAD phasing. However these datasets can be easily solved using
> other experimental phasing method. Instead of using anomalous signal we could use isomorphous signal only. For example RIP or SIR
> phasing method, as there is a difference in intensity between the datasets due to scattering of S and Se. Since frac.80.mtz data contains
> 20% selenium that is sufficient to solve the structure against the frac.100.mtz. It seems the structure can be solved even as less as 10%
> selenium content (frac.90.mtz vs frac.100.mtz), and substructure can be solved easily. This is not surprising, the pair of the datasets is
> quite isomorphous, . We phase all reflections (centric and non-centric) where as anomalous phasing we could phase non-centric reflections
> only. In fact, Single Isomorphous Replacement phasing method is the first phasing technique. This method has been further extended by
> Ravelli et al with some deviation by introduction of X-ray or UV RIP phasing.
>
> I tried RIP (SIR) phasing protocol of Auto-Rickshaw using frac.90.mtz as "before" and frac.100.mtz as "after". Auto-Rickshaw used
> SHELXC/D/E and ARP/wARP/REFMAC5 to get the partially refined model (Rfree below 30%) .
>
> Cheers
> Santosh
>
> Santosh Panjikar, Ph.D.
> Scientist
> Australian Synchrotron
> 800 Blackburn Road
> Clayton VIC 3168
> Australia
> Ph: +61-4-67770851
> ________________________________________
> From: CCP4 bulletin board [[log in to unmask]] On Behalf Of James Holton [[log in to unmask]]
> Sent: Monday, January 14, 2013 8:12 PM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] a challenge
>
> I am absolutely delighted at the response I have gotten to my little
> "John Henry Challenge"! Three people already have managed to do the
> "impossible". Congratulations to George Sheldrick, Pavol Skubak and Raj
> Pannu for finding ways to improve the phases over the ones I originally
> obtained (using the default settings of mlphare and dm) and build their
> way out of it. This is quite useful information! At least it is to me.
>
> Nevertheless, I do think Frances Reyes has a point. This was meant to
> be a map interpretation challenge, and not a SAD-phasing challenge. I
> appreciate that the two are linked, but the reason I did not initially
> provide the anomalous data is because I thought it would be too much to
> ask people to re-do all the phasing, etc. Yes, there do appear to be
> ways to improve the maps beyond the particular way I phased them, but no
> matter how good your phasing program is, there will always be a level of
> anomalous signal that will lead to phases that are "off" enough to make
> building the model "impossible". Basically, once the map gets bad
> enough that just as many "wrong" atoms get built in as "right" atoms,
> then there is no escape. However, I think human beings should still
> have an advantage when it comes to pattern recognition, and I remain
> curious to see if an insightful crystallographer can tip that balance in
> the right direction. I am also still curious to see if tweaking some
> setting on some automated building program will do that too. So, my
> original question remains: are automated building programs better than
> humans? Any human?
>
> I therefore declare the John Henry Challenge still open.
>
>
> But yes, improving the phases can tip the balance too, and the accuracy
> of the anomalous differences will ultimately affect the accuracy of the
> phases, and so on. This is a much broader challenge. And I think the
> best way to frame it is with the question:
> "How low can the anomalous signal be before any conceivable approach fails?"
> and perhaps:
> "What is the best procedure to use for weak anomalous signal?"
>
> For those who are interested in joining George, Pavol, Raj and others
> in this new challenge, the full spectrum of "difficulty" from trivial
> (100% Se incorporation) to a complete waste of time (0% Se, 100% S) is here:
> http://bl831.als.lbl.gov/~jamesh/challenge/occ_scan/
>
> The "impossible.mtz" for the John Henry Map Interpretation Challenge was
> derived from "frac0.79.mtz" and "possible.mtz" from "frac0.78.mtz".
> These simulated 31% and 32% Se incorporation into Met side chains
> (respectively). It has now been shown that both of these can be solved
> automatically if you do the phasing right. But what about frac0.80.mtz?
> Or frac0.90.mtz ? At least on this one "coordinate" of Se
> incorporation, the prowess of a particular approach can be given a
> "score". For example, a "score" of 0.78 means that the indicated
> procedure could solve the frac0.78.mtz dataset, but not the frac0.79.mtz
> dataset.
>
> Based on the reports I have gotten back so far, the "difficulty score"
> lineup is:
>
> score method
> 0.86 xds, xscale, right sites, crank2 (Pavol Skubak)
> 0.78 xds, xscale, right sites, mlphare, dm, phenix.autobuild using 20
> models (James Holton)
> 0.75 xds, xscale, right sites, mlphare, dm, buccaneer/refmac/dm (James
> Holton)
> 0.71 xds, xscale, right sites, mlphare, dm, ARP/wARP 7.3 (James Holton)
> 0.51 xds, xscale, right sites, mlphare, dm, ARP/wARP 6.1.1 (James Holton)
>
> Note that all of these attempts "cheated" on the sites. Finding the
> sites seems to be harder than solving the structure once you've got
> them. That lineup is:
>
> score method
> 0.82 cheating: xds, xscale, right phases, anomalous difference Fourier
> (James Holton)
> 0.79 xds, xscale, shelxc/d/e 3.5A NTRY=10000 (George Sheldrick)
> 0.74 xds, autorickshaw (Santosh Panjikar)
> 0.65 xds, xscale, phenix.hyss --search=full (James Holton)
> 0.60 xds, xscale, shelxc/d with NTRY=100 (James Holton)
>
> Where again the "score" is the dataset where the heavy atom site
> constellation found is close enough to the "right" one to move forward.
> This transition, like the model-building one, is remarkably sharp,
> particularly if you let each step run for a lot of cycles. The graph
> for model-building is here:
> http://bl831.als.lbl.gov/~jamesh/challenge/build_CC_vs_frac.png
> Note how the final map quality is pretty much independent of the initial
> map quality, up to the point where it all goes wrong. I think this
> again is an example of the solution needing to be at least "half right"
> before it can be improved. But perhaps someone can prove me wrong on
> that one?
>
> For those who want the unmerged data, I have all the XDS_ASCII.HKL files
> here:
> http://bl831.als.lbl.gov/~jamesh/challenge/occ_scan/XDS_ASCII.tgz
>
> If you'd like to go all the way back to the images, you can get them
> from here:
> http://bl831.als.lbl.gov/~jamesh/workshop2/
> the "badsignal" dataset is what produced frac1.00.mtz, and "goodsignal"
> produced frac0.00.mtz. You can generate anything in between using the
> provided img_mix.com script.
>
>
> Oh, and when it comes to how useful it is to spend "weeks" building
> manually into a bad map, well I suppose that does indeed depend on what
> alternatives you have and on the science you are trying to do. I agree
> that it is always better to have better data, but if you spend too much
> time trying to improve your crystals and waiting for your next beam
> time, then somebody else who IS willing to build into dodgy maps will
> probably do the science for you and publish it first. So, I think in a
> world of competitive grant renewals it really is critically important to
> know at what point it actually is "impossible" to solve the structure,
> as opposed to a situation where trying some new procedure (or
> collaborator) might be the way to go. I'd like to be able to answer
> that question for my users, and that's why I'm doing this.
>
> -James Holton
> MAD Scientist
>
>
> On 1/13/2013 12:11 PM, jens Preben Morth wrote:
>> I agree with Tassos, and btw think that this crystallographer, should
>> be able to go back into the lab and optimize the present crystal
>> conditions to get better crystals. In particularly, when he or she
>> realize that the scientific question they set out to investigate
>> cannot be answered, by analyzing the final structure, with the
>> available data quality.
>> Preben
>>
>>
>> On 1/13/13 8:52 PM, Anastassis Perrakis wrote:
>>>> 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.
>>> Let me disagree ... An excellent macromolecular crystallographer, is
>>> one that given some crystals can derive the best strategy to collect
>>> data,
>>> process the data optimally, derive phases using all available
>>> information, build a model and refine it in such a way that it best
>>> explains both data
>>> and geometrical expectations, and do these as efficiently as possible.
>>>
>>> Efficiency may suggest using one automated suite or another - or
>>> indeed may best be achieved by manual labor - be it in the map or in
>>> data
>>> collection strategy or refinement or another step: and here I am
>>> ignoring the art of transforming
>>> hair-needle-crystalline-like-dingbits to a diffracting crystal.
>>>
>>> One that can interpret a map with poor phases can be either a genius
>>> in 3d orientation - or a not necessarily too intelligent nor
>>> experienced but determined student
>>> that can drink and breathe this map for a few weeks in a row until a
>>> solution is in place. Neither would make an excellent macromolecular
>>> crystallographer by necessity.
>>>
>>> Tassos
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