[phenixbb] change sigma for an already restrained bond

[Jorge Iulek]

Dear Pavel,

     Thank you; Nigel has also written me, I have tested according to 
your directions and it works. One has to setup up cld=False as you point 
(but this is not needed for angles, dihedrals).
     Sincerely,

Jorge


On 4/18/24 21:35, Pavel Afonine wrote:
> Hi Jorge,
>
> to answer your question and for the record, the following exercise:
>
> phenix.fetch_pdb 1yjp --mtz
> phenix.refine 1yjp.{pdb,mtz} output.prefix=1 params.eff 
> write_final_geo_file=true > & 1.zlog &
> phenix.refine 1yjp.{pdb,mtz} output.prefix=2 params.eff 
> write_final_geo_file=true cdl=false > & 2.zlog &
>
> confirms that you can override standard bond lengths and sigmas.
>
> In the first case I see (both geo files):
>
> User supplied restraints: 1
> Sorted by residual:
> bond pdb=" N   GLN A   5 "
>      pdb=" CA  GLN A   5 "
>   ideal  model  delta    sigma   weight residual
>   1.456  1.459 -0.003 1.21e-02 6.83e+03 4.30e-02
>
> and
>
> User supplied restraints: 1
> Sorted by residual:
> bond pdb=" N   GLN A   5 "
>      pdb=" CA  GLN A   5 "
>   ideal  model  delta    sigma   weight residual
>   1.458  1.458 -0.000 1.19e-02 7.06e+03 2.44e-04
>
> And in the second case I see
>
> User supplied restraints: 1
> Sorted by residual:
> bond pdb=" N   GLN A   5 "
>      pdb=" CA  GLN A   5 "
>   ideal  model  delta    sigma   weight residual
>   2.000  1.459  0.541 1.00e-02 1.00e+04 2.93e+03
>
> and
>
> User supplied restraints: 1
> Sorted by residual:
> bond pdb=" N   GLN A   5 "
>      pdb=" CA  GLN A   5 "
>   ideal  model  delta    sigma   weight residual
>   2.000  1.987  0.013 1.00e-02 1.00e+04 1.79e+00
>
> NOTE the nuance: you need to disable CDL for this to work as you want.
>
> Pavel
>
> On 4/16/24 11:23, Jorge Iulek wrote:
>> 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
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