<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Michał,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>When Chimera reads a PDB file, it adheres to the implied conventions of the PDB — which is what is tripping you up here. The two conventions that are getting you are: (1) consecutive residues in ATOM records with no intervening TER card are connected, and (2) jumps in the residue numbering of consecutive residues along with separation in 3D space imply missing intervening structure. (1) will add extra bonds you didn’t explicitly put in your CONECT records. (2) will change some inter-residue bonds into “missing structure” pseudobonds.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>So if we fix your PDB file, Chimera will like it better. :-) The changes are:</div><div class=""><br class=""></div><div class="">— Change ATOM records to HETATM records</div><div class="">— Put all the atoms into a single residue</div><div class="">— Change the residue name from GLY to UNK</div><div class="">— Give the atoms unique names (I used C0 through C69)</div><div class=""><br class=""></div><div class="">I have attached the edited version of your file.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div></div></div></body></html>