Re: [ccp4bb]: AMORE question

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Wei Zhang wrote:
> 
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> 
> Dear CCP4 users,
> 
> I am now trying to solve a protein structure by  MR using Amore. There are
> four molecules in the au, based on the Matthews'coefficient and
> self-rotation calculation.
> 
> The rotation and translation results are quiet puzzling. Here is the four
> solutions for each molecules, after fixing them one by one
> 
> SOLUTIONTF1  1   77.01   90.00  271.21  0.1013  0.4771  0.3473 46.1 52.5 41.1   2   58.5
> SOLUTIONTF2  1   15.47   48.52   87.74  0.4730  0.1005  0.1464 51.3 51.4 49.9   2   58.5
> SOLUTIONTF3  1   72.38   32.04   96.38  0.8958  0.5205  0.3605 54.2 50.6 52.7   1   59.0
> SOLUTIONTF4  1   81.25   38.07   83.60  0.0458  0.4842  0.3609 56.0 49.5 56.6   1   49.0
> 
> These solutions are the best,even though there is no clear gap.
> 
> After fiting, the CC and R-factor are also improved
> 
>           TABLE   Alpha    Beta   Gamma    Tx      Ty      Tz Corr_F Rfac
> SOLUTIONF     1   76.96   86.29  269.96  0.0895  0.4795  0.3503 57.2 47.8  57.3
> SOLUTIONF     1   17.28   42.06   86.32  0.4720  0.1061  0.1464 57.2 47.8  57.3
> SOLUTIONF     1   73.14   32.34   95.17  0.8981  0.5195  0.3576 57.2 47.8  57.3
> SOLUTIONF     1   79.16   45.90   83.17  0.0539  0.4895  0.3601 57.2 47.8  57.3
> 
> Considering the model I used contains only 60% amino acids of my protein,
> I think it is close to the solution.
> 
> But, problem appears when I check their packing. Molecules overlap to each
> other, either directly or to their symmetry mates.
> 
> My questions are
> 
> 1.Could someone know why such CC and R-f doesn't produce right
> solution?


 Many reasons.. CC and R-f are indicators only.

 Have you got the right space group? Is there translational non-cryst
symmetry? Look at the native 4A Patterson and see if there is a large
peak off the origin.. With 4 molecules in the asymm unit it is common to
find a peak with on coordinate 0.5. And that will generate apparent
absences for a 21 screw although your space group may well have not got
one.

You need then to run the TRAFUN in all possible space groups. 
eg P 21 21 21 and P 2 21 21   if your NCS gave you a peak at x=0.5, ...

Your solution would appear OK because you may well have 2 molecules
correctly placed in the wrong space group..
 If that is true you will probably have found a solution which is half
right - 

OK?
Eleanor