[phenixbb] change sigma for an already restrained bond

[Jorge Iulek]

Hi,

	Well, people are very busy, but maybe one starting information: is 
tightening of one single bond (through its sigma value) meant to be 
possible?
	Thanks!

Jorge

On 4/12/24 16:45, Jorge Iulek wrote:
> 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