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RE: [ccp4bb]: Summary of Replies: Data Reduction for mosaic crystals...
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Greetings,
Tassos has finally got me writing. I agree with him that fine phi slicing is
useless for large mosaicity crystals. I wrote something about it in a very
old CCP4 newsletter, something like 1988 (not wanting to show off too
much!). I was dealing with outrageous mosaicities at the time.
the bottom line is, mosaicity is usually expressed as one number, when in
fact it is anisotropic in a significant number of cases. If the direction of
highest anisotropy is in the phi direction, then no amount of phi slicing is
going to be good enough. Reflections are overlapped in reciprocal space, and
the projection geometry onto the detector will not alleviate the problem.
Seek new less mosaic crystals. Steve Gamblin's trick of using microfocus
beamline on the tip of a crystal circumvents the problem in two ways. The
edge of a crystal must be less mosaic, at least in that case. The microfocus
beamline helped by reducing the cross-fire, which gives a smaller spot
cross-section. He was lucky, but I expect this trick will work for many
cases.
As for the ideal phi width that does not incur spatial overlaps in the x-y
plane, well, here we have two schools of thought. Is it better to get as
many fully recorded, 'safe' in MOSFLM speak, or better to reduce the signal
to background by slicing? The 'calssical' MOSFLM school went as far as
repeating part of each image in the next image to avoid partials altogether,
i.e. Image 1 goes from 0 to 1.2, Image 2 goes from 1.0 to 2.2 etc, and then
use only fulls in scaling. I think we don't need to do that anymore because
the orientation matrix is usually reliable with the current versions of the
algorithms in use. There is an advantage in using a phi width that would
give a reflection distributed over 2 to 3 images, in the 'median range' of
the diffraction pattern (the area half-way between the rotation axis and the
edge of the detector). The idea here is that if a reflection is 0.1 deg wide
(as per the mosaicity) and you use 1 deg frames, then the reflection is in
diffracting position only 10% of the time, and the rest of the time it is
collecting background. You might think that you are getting a good
background measure, but that is only at the expense of swamping the signal.
Having said that, people use that routinely, with little adverse effect. The
counter argument is logistic, why collect 1000 frames when 100 could do!
Again, I think modern technology is good enough to allow us this luxury of
fine phi slicing. Oldsters like me might like to stick to old tried and
tested methods. But, quoting from one recent advert, WHAT IF? should be our
motto. Let's try a few variations and see what new answers we might get. I
know many people have done these tests to exhaustion, but it is the end user
that has to convince themselves in the end.
Well, on this cheerful morning (yes, it's raining again!), I hope I have
provoked some thoughts in your minds. I hope they are useful and helpful. I
also hope that Tassos is now pleased for provoking some discussion. Cheers.
Pierre Rizkallah
-----Original Message-----
From: Anastassis Perrakis [mailto:perrakis@nki.nl]
Sent: 10 June 2002 08:45
To: raji
Cc: ccp4bb@dl.ac.uk
Subject: Re: [ccp4bb]: Summary of Replies: Data Reduction for mosaic
crystals...
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*** CCP4 home page http://www.ccp4.ac.uk ***
> Here are all the responses to my questions! Thank you very much.
> Raji
>
> Questions:
> I am working on a dataset where the crystal has a very high mosaicity - my
> estimate is ~2.0 or more. I have had to take 0.1deg frames during data
Since I am a bit dissapointed that I failed to provoke a good discussion
with my last answer on that one, but I still find it interesting,
I will rephrase my last mail as direct questions and wait for some lively
discussion:
If you DO have crystals with 2.0deg mosaicity:
1. Am I alone thinking Raji did *not 'have had'* to take 0.1deg frames ?
Besides the good ideas offered for really processing the data,
does fine phi slicing improve anything for *very mosaic* crystals ?
2. Do people get good maps out of such datasets ?
3. Have people solved non MR structures out of >1.5 def mosaicity data ?
4. Whats at the end the minimal meangfull phi slice to get as fucntion of
mosaicity ?
5. Any tricks peopel want to share with us for reducing mosaicity
(annealing?) ?
Tassos
P.S. Sorry for continuing this non-ccp4-directly related discussion but I
really
think we can
learn from some comments of people that had similar experiences with very
high
mosaicity - its a problem everybody has seen at some time or the other !
--
NKI, Department of Molecular Carcinogenesis
Plesmanlaan 121 1066 CX Amsterdam NL
Phone +31-20-512-1951 Fax +31-20-512-1954
SMS: +31-6-28597791 WWW: http://den.nki.nl