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

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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