Re: [ccp4bb] crystal problems

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

Previous message:
Subject: crystal problems
From: "Benirschke, Robert C {- dot -} " Benirschke {- dot -} Robert {- at -} MAYO {- dot -} EDU
Date: 2007-05-29

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From: "Deng, Junpeng" junpeng {- dot -} deng {- at -} OKSTATE {- dot -} EDU
Date: 2007-05-29

Subject: Re: crystal problems
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-29

Detwinning without a known structure, and such a high twin factor must
be very unreliable .

If you have only IT1 and IT2, the detwin algorithm gives I1 = (TF*It1
+ (1-TF)*IT2) / (1-2*TF)

(Maybe signs wrong there!) Since (1-2*TF) is almost 0, this is pretty
inaccurate..

But if you have a structure already and can calculate I1(calc) and
I2(calc), the detwinning keeps the calculated ration of
I1(calc)/I2(calc) and gets a much better estimate of I1 and I2.

So it isnt surprising you P6 twinned map looks better than one
calculated against detwinned P3 data.

Re the gap - I dont know.
Did you test to see if there was a pseudo translation vector or any
other strange features to the data.
Eleanor

Benirschke, Robert C. wrote:
>
> Dear All,
>
> I had written earlier about my twinned crystal that was giving me
> problems......thanks to all who responded, it was very helpful. I
> have another couple questions about the same crystal that is confusing
> us. The twinned crystals space group is P3. Twinning was found using
> the Yeates twinning server and the twin fraction of different crystals
> ranged from .32-.48. Crystals with the lower twin fraction diffracted
> to a much lower resolution and the more twinned crystals diffracted to 3.
>
> Using the data from the .48 twinned crystal I refined into the twinned
> P6 data (what we believed to be the space group originally) as well as
> the detwinned P3 data. The result of this is that both are about the
> same as far as R/Rfree (.28/.36) and the P6 is better as far as
> structure geometry and density fit. Why is this the case? Does the
> detwinning process introduce more error than if one just refined into
> the twinned data? Is truncate and the twinning server ever wrong in
> their diagnosis of twinning?
>
> Secondly, this structure still has an area of missing density parallel
> to the a-b plane which never resolves (1/6 at top and bottom along
> c). This is the case for twinned, detwinned, P6, P3, and everything
> else I have tried. It is also seen as P1, so we are not averaging out
> weak reflections when scaling in different groups. I have also
> searched these areas with FFEAR which yields nothing substantial.
> This area is where many long disordered chains point (nearly 30
> residues), so one of our thoughts is that there are many different
> conformations of these tails that point into this area. Is this
> possible? It seems to me that this would be a situation that promotes
> twinning as well. Our second idea is that there is a translation of
> 1/6 a unit cell along c that would allow the rest of the cell to be
> resolved as long as that plane of empty density is filled with same
> contents. Would this be possible? Any ideas of how to test each of
> these possibilities? Can anyone think of any other ideas.?
>
> I´m sure I´ve said things that are unclear, so if clarification is
> needed please let me know.
>
> Thanks,
>
> Robert
>

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

Previous message:
Subject: crystal problems
From: "Benirschke, Robert C {- dot -} " Benirschke {- dot -} Robert {- at -} MAYO {- dot -} EDU
Date: 2007-05-29

Next message:
Subject: post-doc position opening
From: "Deng, Junpeng" junpeng {- dot -} deng {- at -} OKSTATE {- dot -} EDU
Date: 2007-05-29