.@lbl.gov]
Sent: Monday, January 14, 2013 8:12 PM
To: CCP4BB@JISCMAIL.AC.UK
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 Geor
d [CCP4BB@JISCMAIL.AC.UK] On Behalf Of James Holton
> [jmhol...@lbl.gov]
> Sent: Monday, January 14, 2013 8:12 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] a challenge
>
> I am absolutely delighted at the response I have gotten to my little
> "John Henry Challe
Dear James
> I actually chose 3dko because it is a kinase (with a ligand), and
> therefore an interesting candidate for a molecular replacement
> "score". I have not set this up yet, but I think if you look for PDB
> entries that contain the word "kinase" and try to molecular-replace
> all of the
lletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of James Holton
[jmhol...@lbl.gov]
Sent: Monday, January 14, 2013 8:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] a challenge
I am absolutely delighted at the response I have gotten to my little
"John Henry Challenge"! Three people
I actually chose 3dko because it is a kinase (with a ligand), and
therefore an interesting candidate for a molecular replacement
"score". I have not set this up yet, but I think if you look for PDB
entries that contain the word "kinase" and try to molecular-replace
all of them into the 3dko datase
On Mon, Jan 14, 2013 at 11:18 AM, Tim Gruene wrote:
> I admit not having read all contributions to this thread. I understand
> the "John Henry Challenge" as whether there is an 'automated way of
> producing a model from impossible.mtz'. From looking at it and without
> having gone all the way to a
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Hello James and all other contributors,
I admit not having read all contributions to this thread. I understand
the "John Henry Challenge" as whether there is an 'automated way of
producing a model from impossible.mtz'. From looking at it and without
h
"What is the best procedure to use for weak anomalous signal"
That opens up the can of worms which I'm happy to jump into.
We've had very good success in the years 2003-2009 with shelx for finding sites
(sometimes more than 1 trials) then force feeding them to sharp for phase
improvement. We
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 (us
Since the discussion for crystallographers is fired up. I want to put on
record that I totally agree with Tassos about the profile of a
crystallographer. If you take away the crystals, then a crystallographer
is no long a crystallographer.
Demetres
On 13/1/2013 9:52 μμ, Anastassis Perrakis w
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
analy
> 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
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
I have now looked at James's two challenges to see what I could learn
from them, and will try to give enough details so that less experienced
readers of this list can repeat what I did and apply the experience
thereby gained to solving their own structures. For those who are not
interested in
I can build from the impossible.mtz data in the following two steps:
1. getting the SE substructure from anomalous difference map
constructed from impossible.mtz
2. running "combined" model building using the substructure
from step 1 and starting from the impossible.mtz map
Only impossible.mtz a
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 pic
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 t
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/~j
Fair enough!
The heavy atom positions are simply the "S" atoms in 3dko. There are 22
of them. Also, in this case the Met side chains (12 of those) are 32%
occupied with Se. The other 68% is sulfur. I think it is "realistic"
that one could know the extent of Se incorporation ahead of time
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)
Dear James,
I agree with Pavel that your example is not very realistic. In practice
one would start from the heavy atom positions. As well as providing
starting phases, they are useful in other ways. For example. shelxe
(and probably most other tracing programs) adds them to a 'no-go'
map so it k
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, t
Hi James,
As an aside (as your point is looking for a John Henry, not investigating
automated model-building) I would point out that it is not uncommon at all to
find cases where a very small difference in starting parameters or starting
phases leads to a very different final result in automate
I have a challenge for all those expert model-builders out there: can
you beat the machine?
It seems these days that everything is automated, and the only decision
left for a crystallographer to make is which automation package to use.
But has crystallography really been "solved"? Is looking
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