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" mailto:pafonine@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" 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
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Pavel Afonine