<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Kate,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">On Mar 4, 2020, at 4:03 PM, Kate Kim <<a href="mailto:kimsk@msg.ucsf.edu" class="">kimsk@msg.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hello,</div><div class=""><br class=""></div><div class="">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 class=""></div><div class=""><br class=""></div><div class="">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 class=""></div><div class=""><br class=""></div><div class="">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 class=""></div><div class=""><br class=""></div><div class="">Does Chimera need something else other than the LINK record in the PDB to display the bond? <br class=""></div><div class=""><br class=""></div><div class="">Thank you,</div><div class="">Kate<br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div></div>
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