[phenixbb] rigid body refinement problem

Jianghai Zhu jzhu at idi.harvard.edu
Sat Jan 16 17:58:34 PST 2010


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









More information about the phenixbb mailing list