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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 class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></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>
<br>
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