[phenixbb] change sigma for an already restrained bond

[Jorge Iulek]

Dear all,

	I would like to change the sigma value for an already restrained  bond.
	I enter for phenix.refine:
"
     bond {
       action = add delete *change
       atom_selection_1 = chain D and resid 493 and name CA
       atom_selection_2 = chain D and resid 493 and name CB
       symmetry_operation = None
       distance_ideal = 1.532
       sigma = 1.02e-2
       slack = None
       limit = -1.0
       top_out = False
     }

"

	In the log I get:

"
...
   Custom bonds:
     bond:
       atom 1: "ATOM  14355  CA  ALA D 493 .*.     C  "
       atom 2: "ATOM  14358  CB  ALA D 493 .*.     C  "
       symmetry operation: x,y,z
       distance_model:   1.511
       distance_ideal:   1.532
       ideal - model:    0.021
       slack:            0.000
       delta_slack:      0.021
       sigma:            0.0102
     Total number of added/changed bonds: 1
...
"

	But in the .geo file I read:

"
User supplied restraints: 1
Sorted by residual:
bond pdb=" CA  ALA D 493 "
      pdb=" CB  ALA D 493 "
   ideal  model  delta    sigma   weight residual
   1.532  1.511  0.022 1.28e-02 6.10e+03 2.85e+00
"
	1.28e-02 is the default value.

	On the other hand, sigma changes for angles and dihedrals seem to work 
as expected (the intended values are echoed to the .geo file).
	To add up, if a bond is *added*, the value is in the .geo file.

	I observe this for both
1.20.1-4487
1.21-5207
	versions.

	So, in short, should I be allowed to *change the sigma* for a specific 
*bond*? How should I do it?
	Thanks

Jorge