Re: [ccp4bb] Twinning

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Twinning
From: Rana Refaey dr_rr81 {- at -} HOTMAIL {- dot -} COM
Date: 2009-08-03

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Subject: resolution shells for each bin in scala?
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2009-08-03

Subject: Re: Twinning
From: Matthew Franklin Matthew {- dot -} Franklin {- at -} IMCLONE {- dot -} COM
Date: 2009-08-03

> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Rana Refaey
> Sent: Monday, August 03, 2009 12:26 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Twinning
>
> Hi all,
> I have a few datasets that I think are twinned for several reasons.
> 1)The Rfree and Rmerge are both stuck very high.
> 2) The L-test for twinning in Scala shows twinning
> 3) Also the centric and acentric movements suggest twinning.
> 4) The spots do not match the predication from Mosflm (Non-merohedral
> twinning ?)
>

Hi Rana -

It would be good to rule out one basic problem which is suggested by your item #4. Do you find that a lot of spots don't match the predictions? Or is it just one or two per image? Do the empty predictions have a spot nearby? Does it seem to be in the same lattice as the predicted spots, just offset? This would indicate mis-indexing, probably due to a bad value for the location of the direct beam. This would also be evident in very bad merging R factors. You say Rmerge is bad in item #1 - did you mean that, or did you mean the refinement R factor?

Epitaxial twinning will indeed produce a second pattern of spots which is not aligned with the main lattice. This is usually apparent from looking at the images, and can generally be handled by the indexing and integration programs - again, look at the merging R factor for signs of a problem. What is much harder to deal with is a cracked crystal - the two (or more) cracked pieces are no longer perfectly aligned and will produce split or smeared spots which overlap in some areas/orientations, but not others. I've never had much success working with data like that, and in fact I have a project crippled by this problem right now. (It's NOT the twinning issue I asked about recently - those spots look fine!)

If you're confident that your data is neither mis-indexed nor from a cracked crystal, then we can consider twinning. I'm still working through the guidance suggested to me earlier, so I've got no suggestions on that front. But if your initial intensities are bad due to indexing or crystal problems, you'll never get a well-refined structure.

Hope that helps,
Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems,
a wholly owned subsidiary of Eli Lilly & Company
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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Twinning
From: Rana Refaey dr_rr81 {- at -} HOTMAIL {- dot -} COM
Date: 2009-08-03

Next message:
Subject: resolution shells for each bin in scala?
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2009-08-03