[phenixbb] change sigma for an already restrained bond

[Pavel Afonine]

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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