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CCP4BB  March 2012

CCP4BB March 2012

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Subject:

Re: an ambiguous result of molecular replacement

From:

Randy Read <[log in to unmask]>

Reply-To:

Randy Read <[log in to unmask]>

Date:

Fri, 30 Mar 2012 09:02:56 +0100

Content-Type:

text/plain

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text/plain (59 lines)

Hi,

Do you mean that the second molecule is always overlapped with the first, by saying that it shifts several Angstrom along the x axis?  If there were a larger translation, then what you're seeing would be consistent with translational NCS (tNCS), but the translation should be large enough to shift the second copy off the first!

If you did have tNCS, then the version of Phaser currently distributed with CCP4 would have trouble dealing with it.  We have a new version that accounts well for the statistical effects of tNCS.  It's available in current releases of Phenix and will soon be available with the upcoming CCP4 release.  Alternatively, the version of Molrep in the current CCP4 has its own treatment for tNCS.

However, if it's really a small vector, then it's more likely that something else is going on.  You could have some kind of lattice translocation disorder.  The crystal could be twinned so the real symmetry could be lower, or even some combination of the above.

Good luck sorting it out!

Best wishes,

Randy Read

On 30 Mar 2012, at 05:22, Zhiyi Wei wrote:

> Dear all,
> 
> I got a weird solution from Phaser. The background is that, space
> group C2221, resolution ~4A, in complex with a peptide, and having a
> apo form structure as the search model. Phaser gave two rotation
> function peaks with Z > 7. But when searching translation function
> peaks, Phaser gave many high Z score peaks listed below rather than a
> single solution. These peaks share same fraction Y&Z but with
> different X. Most of them pasted the packing validation. The when
> searching the second copy, each solutions have a single translation
> peak that showed very high Z score (> 20). I check some of these
> solutions in Coot, and found that the two copies of each solution has
> the same relative orientation and each solution shifts several
> angerstroms in X axis. I also tried C222 and did not get better result
> than C2221. Any comments or suggestion? Thanks a lot!
> 
> Best,
> Zhiyi
> 
>   #     (#)   Frac X Frac Y Frac Z   LLG   Z-score Split #Group    raw/top
>   1     1      0.155  0.436  0.287 +219.80   11.17     0      1 272.58/272.58
>   2     2      0.350  0.436  0.287 +211.92   10.53    24      1 267.42/267.42
>   3     3      0.542  0.436  0.287 +211.31   10.48    44      1 266.05/266.05
>   4     5      0.579  0.436  0.287 +209.66   10.34    40      2 260.14/260.14
>   5     12     0.267  0.436  0.287 +209.11   10.30    14      2 256.53/256.53
>   6     4      0.224  0.435  0.288 +208.41   10.24     8      2 261.39/261.39
>   7     11     0.485  0.436  0.287 +208.28   10.23    40      2 256.95/257.13
>   8     7      0.191  0.435  0.287 +205.18    9.97     4      2 258.95/258.95
>   9     15     0.400  0.436  0.287 +201.90    9.70    30      2 254.20/254.20
>   10    9      0.297  0.437  0.287 +201.79    9.69    17      1 257.75/257.75
>   11    16     0.449  0.436  0.287 +198.77    9.45    36      1 252.80/252.80
>   12    17     0.129  0.437  0.287 +195.66    9.19     3      1 252.41/252.41
>   13    20     0.377  0.436  0.287 +194.95    9.13    27      1 246.37/246.37
>   14    21     0.422  0.436  0.287 +190.72    8.78    33      1 245.42/245.42
>   15    19     0.521  0.437  0.287 +190.22    8.74    45      1 246.46/246.46

------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
Hills Road                                    E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk

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