[phenixbb] pdb LINK record lost after phenix refine in GUI
pafonine at lbl.gov
Thu Jul 16 18:45:24 PDT 2015
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?
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 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.
> 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 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).
>> 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:
>>> 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
>>> Unsubscribe:phenixbb-leave at phenix-online.org
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