[phenixbb] rigid body refinement problem

[Jianghai Zhu]

Hi Pavel,

Did you get my files?  and any news? Thanks.

-- Jianghai






On Jan 16, 2010, at 10:20 PM, Pavel Afonine wrote:

> 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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