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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">
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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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