<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 Hong,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>When I open 1WWW and save it as a PDB, there are TER cards after all 4 chains, so it must be something specific to your structure. So I would need access to the structure to figure out why there is no TER card. You could use Help→Report A Bug in ChimeraX and attach the file, or, if your want the file to remain private you could email it to me directly. Without the file I don't know if there's much I can do.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><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><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 21, 2022, at 8:30 AM, HONG ZHAN via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">Hi Elaine,<span class="Apple-converted-space"> </span><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">I am uploading to the EMDB (wwPDB Deposition) and I am doing a composite deposition.<span class="Apple-converted-space"> </span><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">I saw there are TER XXXX after each chain but lack in the Chain X.<span class="Apple-converted-space"> </span><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">Thanks,<span class="Apple-converted-space"> </span><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">Hong<br class=""></span></div><div id="appendonsend" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""></div><hr tabindex="-1" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; display: inline-block; width: 483.125px;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, December 21, 2022 10:27 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>HONG ZHAN <<a href="mailto:hzhan3@wisc.edu" class="">hzhan3@wisc.edu</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimerax-users] PDB upload TER card error</font><div class=""> </div></div><div class="BodyFragment" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><font size="2" class=""><span style="font-size: 11pt;" class=""><div class="PlainText">Hi Hong,<br class="">Uploaded where? We try to write correct PDB format, but some websites that use uploaded PDBs may be pickier than others.<br class=""><br class="">Anyway, the solution is exactly what the error message says:<br class="">Just use your favorite text-editor to add a line with first 3 characters TER after the X chain coordinates (ATOM lines).<br class=""><br class="">Intro to PDB format:<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <span class="Apple-converted-space"> </span><br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class="">> On Dec 21, 2022, at 6:56 AM, HONG ZHAN via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class="">><span class="Apple-converted-space"> </span><br class="">> Dear all,<span class="Apple-converted-space"> </span><br class="">><span class="Apple-converted-space"> </span><br class="">> I saved my protein coordinates in ChimeraX as pdb (it has multiple chains), however, when I was doing upload on the PDB, it shows this error, I am using ChimeraX 1.5rc202211091945 on Linux ubuntu 22.04 LTS.<span class="Apple-converted-space"> </span><br class="">><span class="Apple-converted-space"> </span><br class="">> Coordinates issues:<span class="Apple-converted-space"> </span><br class="">><span class="Apple-converted-space"> </span><br class="">> ERROR: There is no TER card at the end of polymer chain 'X'. All polymer chains should have a TER card at the end of each chain. Please add TER card and restart again.<br class="">><span class="Apple-converted-space"> </span><br class="">> Many thanks!<br class="">> Hong<br class=""><br class=""></div></span></font></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">ChimeraX-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a></span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></span></div></blockquote></div><br class=""></div></body></html>