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Hi Lu,<br>
<br>
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?<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/16/15 18:38, luzuok wrote:<br>
</div>
<blockquote
cite="mid:6d1adf7e.2911.14e99a9491b.Coremail.luzuokun@126.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div>Dear Pavel,</div>
<div> Thank you for your explanation.</div>
<div> 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.<br>
</div>
It seems that the riding H of C23 cannot see the OG
neighbouring to it.<br>
<br>
Best wishes!<br>
Lu<br>
<br>
<br>
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<div style="color: rgb(51, 51, 51); font-family: 'Microsoft
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19.992000579834px;">南开大学新生物站A202</div>
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<div style="color: rgb(51, 51, 51); font-family: 'Microsoft
Yahei', verdana; font-size: 12px; line-height:
19.992000579834px;">Lu Zuokun, Ph.D. Candidate</div>
<div style="color: rgb(51, 51, 51); font-family: 'Microsoft
Yahei', verdana; font-size: 12px; line-height:
19.992000579834px;">College of Life Science, Nankai
University</div>
</div>
<br>
At 2015-07-16 23:07:49, "Pavel Afonine" <<a
moz-do-not-send="true" href="mailto:pafonine@lbl.gov"><a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a></a>>
wrote:<br>
<blockquote id="isReplyContent" style="PADDING-LEFT: 1ex;
MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> Hi
Lu,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/16/15 00:54, luzuok wrote:<br>
</div>
<blockquote
cite="mid:7c465e6f.1ae69.14e95db8799.Coremail.luzuokun@126.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><br>
<div>Dear Pavel and Nigel,<br>
<br>
I can see:<br>
<br>
</div>
bond pdb=" OG SER A 265 "<br>
pdb=" C23 AIX A 700 "<br>
ideal model delta sigma weight residual<br>
<div> 1.330 1.339 -0.009 2.00e-01 2.50e+01 2.16e-03<br>
<br>
I think this bond is what I want.<br>
<br>
If I want to _see_ this bond in graphical tool, like
coot or pymol, Do I have to add a link record in PDB?<br>
<br>
You are right Nigel, I made a mistake of python and
Phenix version.<br>
<br>
Best withes!<br>
Lu<br>
<br>
</div>
<div style="position:relative;zoom:1">--<br>
<br>
<div style="color: rgb(51, 51, 51); font-family:
'Microsoft Yahei', verdana; font-size: 12px;
line-height: 19.992000579834px;">Lu Zuokun, Ph.D.
Candidate</div>
<div style="color: rgb(51, 51, 51); font-family:
'Microsoft Yahei', verdana; font-size: 12px;
line-height: 19.992000579834px;">College of Life
Science, Nankai University</div>
</div>
<br>
在 2015-07-16 14:21:24，"Pavel Afonine" <a
moz-do-not-send="true" class="moz-txt-link-rfc2396E"
href="mailto:pafonine@lbl.gov"><a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a></a>
写道：<br>
<blockquote id="isReplyContent" style="PADDING-LEFT:
1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px
solid"> All connectivity information is in .geo file:
check it to see if the bind in question is present
there.<br>
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).<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/15/15 18:04, luzuok
wrote:<br>
</div>
<blockquote
cite="mid:46b7ca4c.1227a.14e9464638f.Coremail.luzuokun@126.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div>Dear all, <br>
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).<br>
Do you think this is a real bond? How to
maintain this record?<br>
Any comment is appreciated!<br>
Best regards!<br>
<br>
Data resolution: 2.4<br>
Phenix version:v2.7<br>
<br>
phenix refine log:<br>
======================== Summary of geometry
restraints =======================<br>
<br>
Number of disulfides: simple=1, symmetry=0<br>
Simple disulfide: pdb=" SG CYS A 482 " -
pdb=" SG CYS A 484 " distance=2.04<br>
Custom bonds:<br>
bond:<br>
atom 1: "ATOM 1205 OG SER A 265
.*. O "<br>
atom 2: "HETATM 3413 C23 AIX A 700
.*. C "<br>
symmetry operation: x,y,z<br>
distance_model: 1.339<br>
distance_ideal: 1.330<br>
ideal - model: -0.009<br>
slack: 0.000<br>
delta_slack: -0.009<br>
sigma: 0.2000<br>
Total number of custom bonds: 1<br>
Time building geometry restraints manager:
0.20 seconds<br>
<br>
pdb file LINK record:<br>
LINK OG SER A 265 C23
AIX A 700 1555 1555 <br>
<br>
</div>
<br>
<div style="position:relative;zoom:1">--<br>
<div style="color: rgb(51, 51, 51); font-family:
'Microsoft Yahei', verdana; font-size: 12px;
line-height: 19.992000579834px;"><br>
</div>
<div style="color: rgb(51, 51, 51); font-family:
'Microsoft Yahei', verdana; font-size: 12px;
line-height: 19.992000579834px;">Lu Zuokun,
Ph.D. Candidate</div>
<div style="color: rgb(51, 51, 51); font-family:
'Microsoft Yahei', verdana; font-size: 12px;
line-height: 19.992000579834px;">College of
Life Science, Nankai University</div>
</div>
</div>
<br>
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