<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 style="clear:both"></div></div><div id="divNeteaseMailCard"></div><br>�� 2015-07-16 14:21:24��"Pavel Afonine" <pafonine@lbl.gov> ���<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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