[phenixbb] pdb LINK record lost after phenix refine in GUI

[luzuok]

Dear Pavel,
    The serine contains no H atoms and the ligand has H atoms in the PDB file. How do Phenix refine deal with this two kind of H atoms at nearly the same place?

I have deleted the H atoms of the ligand, and refined again. The coordinate is reasonable without H atoms being seen.

So, I think the simplest way is to delete all H atom in such resolution.

Best wishes!

Lu






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卢作焜
南开大学新生物站A202


Lu Zuokun, Ph.D. Candidate
College of Life Science, Nankai University

在 2015-07-17 09:45:24，"Pavel Afonine" <pafonine at lbl.gov> 写道：
Hi Lu,

could it be that you define a conflicting restraint? On one hand you want that O-C bond to be 1.44A (that's what I see on your picture), on the other hand you want that H to be reasonable distance apart from O (and not 1.14A). I would guess if you want to define that bond you nee to delete H first. Could this explain what you observe?

Pavel


On 7/16/15 18:38, luzuok wrote:

Dear Pavel,
    Thank you for your explanation.
    After adding the bond restrain and refinement, the position of the hydrogen from the bonded atom of the ligand seems not reasonable. This hydrogen is too close to the other bonded atom. I can even see this H atom links to two atom.

    It seems that the riding H of C23 cannot see the OG neighbouring to it.

Best wishes!
Lu



--

卢作焜
南开大学新生物站A202


Lu Zuokun, Ph.D. Candidate
College of Life Science, Nankai University

At 2015-07-16 23:07:49, "Pavel Afonine" <pafonine at lbl.gov> wrote:
Hi Lu,

seeing the link in graphics and actually having bond defined in refinement are two different things. Refinement uses standard restraints and those you define on top of that. Visualization tools use standard bonding patterns to show you the bonds (and sometimes also use distance based connectivity, such as Pymol). Visualization tools are unlikely to guess anything on top of that.

So if you want to have specific bond in refinement, then tell refinement program to add it (and checking .geo file is not a bad idea to verify that it was actually added). Seeing that bond on graphics is a different story and it is outside the scope of Phenix refinement. Check documentation of visualization program you use to learn what's required to see what you want to see.

Pavel


On 7/16/15 00:54, luzuok wrote:



Dear Pavel and Nigel,

    I can see:


bond pdb=" OG  SER A 265 "
         pdb=" C23 AIX A 700 "
  ideal  model  delta    sigma   weight residual

  1.330  1.339 -0.009 2.00e-01 2.50e+01 2.16e-03

I think this bond is what I want.

If I want to _see_ this bond in graphical tool, like coot or pymol, Do I have to add a link record in PDB?

You are right Nigel, I made a mistake of  python and Phenix version.

Best withes!
Lu


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Lu Zuokun, Ph.D. Candidate
College of Life Science, Nankai University

在 2015-07-16 14:21:24，"Pavel Afonine" <pafonine at lbl.gov> 写道：
All connectivity information is in .geo file: check it to see if the bind in question is present there.
phenix.refine does not read/write LINK records given that all info is in .geo file, and input (custom) linking is specified via custom bonds using atom selection syntax (or clicking in the GUI).

Pavel


On 7/15/15 18:04, luzuok wrote:

Dear all,  
Although Custom geometry restrains was added (see log). After phenix refine, the link record was lost and there seem no bond between this two atoms (1.44 angstrom).
Do you think this is a real bond? How to maintain this record?
Any comment is appreciated!
Best regards!

Data resolution: 2.4
Phenix version:v2.7

phenix refine log:
    ======================== Summary of geometry restraints =======================

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 482 " - pdb=" SG  CYS A 484 " distance=2.04
  Custom bonds:
    bond:
      atom 1: "ATOM   1205  OG  SER A 265 .*.     O  "
      atom 2: "HETATM 3413  C23 AIX A 700 .*.     C  "
      symmetry operation: x,y,z
      distance_model:   1.339
      distance_ideal:   1.330
      ideal - model:   -0.009
      slack:            0.000
      delta_slack:     -0.009
      sigma:            0.2000
    Total number of custom bonds: 1
  Time building geometry restraints manager: 0.20 seconds

pdb file LINK record:
LINK         OG  SER A 265                 C23 AIX A 700     1555   1555  




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Lu Zuokun, Ph.D. Candidate
College of Life Science, Nankai University





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