[phenixbb] change sigma for an already restrained bond

[Jorge Iulek]

According to my current tests, yes. Thanks.
Just correcting my mistyping, one has to setup like you mention: cdl=False.

J.

On 4/18/24 22:09, Pavel Afonine wrote:
>
> Hi Jorge,
>
> great you got an answer from Nigel. I have not seen any reply on the 
> phenixbb list so I replied as well. OK, it sounds like the problem is 
> solved!
>
> All the best!
> Pavel
>
> On 4/18/24 18:00, Jorge Iulek wrote:
>> 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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>>
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