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

[Pavel Afonine]

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 
> <mailto: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
>>
>>     --
>>
>>     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
>>>
>>>
>>>         --
>>>
>>>         Lu Zuokun, Ph.D. Candidate
>>>         College of Life Science, Nankai University
>>>
>>>
>>>
>>>
>>>         _______________________________________________
>>>         phenixbb mailing list
>>>         phenixbb at phenix-online.org
>>>         http://phenix-online.org/mailman/listinfo/phenixbb
>>>         Unsubscribe:phenixbb-leave at phenix-online.org
>>
>>
>>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150716/a5074264/attachment.htm>