[phenixbb] rigid body refinement problem

Pavel Afonine PAfonine at lbl.gov
Sat Jan 16 19:20:23 PST 2010


Hi Jianghai,

I'm replying from an inconvenient place so I cannot give you more 
details (I cannot look at the source code right now). From what I recall 
I'm guessing that this is because the rigid-body procedure has internal 
check that makes sure the shifts applied to the model during refinement 
result in reduced R-factor computed for all reflections. If this check 
fails then the shifted coordinates are re-set to the starting ones (so 
you get the same model in the end).

If you need more details please send me the model, data and the command 
you used, and then I may be able to reproduce and explain details of 
what you observe.

Pavel.


On 1/16/10 5:58 PM, Jianghai Zhu wrote:
> Hi,
>
> I am using phenix.refine_dev_282 for a rigid body refinement.  The output pdb file is exactly the same as the input model even though there are obviously some large movements.  Here are some information from the log file.
>
> Information about total rigid body shift of selected groups:
>                              rotation (deg)                 translation (A)
>                           xyz              total           xyz          total
>   group    1:    0.051   -5.493   -1.073    5.60    0.55  -3.15  -1.35   3.47
>   group    2:    0.254    0.562    0.252    0.67    0.36  -3.99   0.87   4.10
>   group    3:    3.807    4.001   -2.262    5.92   -0.81  -3.17   1.06   3.44
>   group    4:    2.275   -4.215    1.909    5.12   -0.18  -2.95  -1.43   3.28
>   group    5:   -1.902   -5.750   -3.206    6.81   -1.99  -4.44   0.27   4.88
>   group    6:   -4.932   -3.939   -5.340    8.16   -0.18  -2.08  -0.25   2.11
>   group    7:   -1.140   -0.769   -7.715    7.83    0.73  -2.91   0.04   3.00
>   group    8:    2.008   -1.858   -1.236    3.02   -1.10  -5.44  -0.82   5.61
>
>
> But then the model didn't change at all.
>
>  stage        Deviation of refined
>               model from start model
>                max      min     mean
>    0    :    0.000    0.000    0.000
>    1_bss:    0.000    0.000    0.000
>    1_rbr:    0.000    0.000    0.000
>    1_bss:    0.000    0.000    0.000
>    1_adp:    0.000    0.000    0.000
>    1_bss:    0.000    0.000    0.000
>
> Is this a bug?
>
> -- Jianghai
>
>
>
>
>
>
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