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<p>Remove the trailing DCR-CYS in your LINK records, they are
illegal. If you look at the PDB's 1F88's LINK records, they are
of the form:</p>
<p>LINK C1 NAG B 602 O4 NAG B 601
1555 1555 1.38<br>
LINK C1 NAG B 802 O4 NAG B 801
1555 1555 1.39<br>
</p>
<p>So where you have DCR-CYS, Chimera is expecting a numerical
symmetry operator. The PDB format specification is published at
<a class="moz-txt-link-freetext" href="http://www.wwpdb.org/documentation/file-format">http://www.wwpdb.org/documentation/file-format</a>. In general, for
PDB files, not specifying something, rather than putting in
"random" characters, works better.</p>
<p> Good luck,</p>
<p> Greg<br>
</p>
<div class="moz-cite-prefix">On 3/4/2020 6:36 PM, Kate Kim wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMArPweL_HjBVHY=Ck4ocmh6_sENtHfdjfLJ6rxmF+YggpWLOA@mail.gmail.com">
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<div>Hi Elaine and Eric,</div>
<div><br>
</div>
<div>Thank you for your reply.</div>
<div><br>
</div>
<div>I tried to follow the example of 1F88, and I have:</div>
<div><br>
</div>
<div>LINK C1 DCR A 1101 SG CYS A 267
DCR-CYS <br>
LINK C1 DCR B 1201 SG CYS B 267
DCR-CYS</div>
<div>ATOM 7896 SG CYS B 267 149.139 168.091 151.319
1.00 24.38 S<br>
ATOM 1371 SG CYS A 267 174.729 167.809 164.051 1.00
27.17 S</div>
<div>HETATM 6472 C1 DCR A1101 174.148 169.497 163.870
1.00 30.17 C<br>
HETATM12696 C1 DCR B1201 148.862 169.613 152.232 1.00
29.68 C</div>
<div>CONECT 1371 6472<br>
CONECT 7896 12696</div>
<div><br>
</div>
<div>The log says, <br>
</div>
<div>warning: Ignored bad PDB record found on line 148<br>
</div>
<div>warning: Ignored bad PDB record found on line 149</div>
<div><br>
</div>
<div>Lines 148 & 149 refer to the two LINK records. Why is
it saying that it is bad? Does my LINK record (obtained from
Jligand) need to be altered for Chimera?</div>
<div><br>
</div>
<div>Thank you.</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Mar 4, 2020 at 4:35 PM
Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu"
moz-do-not-send="true">meng@cgl.ucsf.edu</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi
Kate,<br>
An example is 1F88 (rhodopsin) where there is both a LINK
record and a CONECT record for the bond between lysine NZ and
the retinal chromophore. Excerpted lines from that PDB file:<br>
<br>
LINK NZ LYS A 296 C15 RET A 977
1555 1555 1.46<br>
<br>
ATOM 2321 NZ LYS A 296 51.283 12.449 -8.206 1.00
26.12 N<br>
<br>
HETATM 5145 C15 RET A 977 52.545 11.720 -8.232 1.00
25.08 C<br>
<br>
CONECT 2321 5145<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Mar 4, 2020, at 4:22 PM, Eric Pettersen <<a
href="mailto:pett@cgl.ucsf.edu" target="_blank"
moz-do-not-send="true">pett@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hi Kate,<br>
> If the connectivity of the DCR residue is specified
in CONECT records (which it probably is), you may have to add
a CONECT record (or add to the existing CONECT record for the
DCR carbonyl carbon) specifying the bond you want. If the
LINK were between standard residues (which don’t have CONECT
records), then I believe the LINK by itself would work.<br>
> One other thing to do is to look at the reply log
(Favorites→Reply Log) and see if there are any complaints when
you open the file.<br>
> <br>
> —Eric<br>
> <br>
> Eric Pettersen<br>
> UCSF Computer Graphics Lab<br>
> <br>
>> On Mar 4, 2020, at 4:03 PM, Kate Kim <<a
href="mailto:kimsk@msg.ucsf.edu" target="_blank"
moz-do-not-send="true">kimsk@msg.ucsf.edu</a>> wrote:<br>
>> <br>
>> Hello,<br>
>> <br>
>> I would like to visualize a thioester bond between a
CYS residue of my protein and a carbonyl carbon of ligand
(DCR) in my model. <br>
>> <br>
>> I have a LINK record for the DCR-CYS thioester bond
created from Jligand and inserted in the PDB right before the
CRYST1 line. <br>
>> <br>
>> However, when I open this PDB in Chimera, the
thioester linkage is not drawn. The distance between the C1 of
DCR and SG of CYS is 1.79 angstrom. <br>
>> <br>
>> Does Chimera need something else other than the LINK
record in the PDB to display the bond? <br>
>> <br>
>> Thank you,<br>
>> Kate<br>
>> <br>
<br>
</blockquote>
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