<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 ChuHui,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Each model in the file has many different residues with the same residue and chain ID and Chimera can’t handle that when trying to match the atoms in later models to those in earlier models. For example, each model in the file has a residue 3864 as a water with no chain ID, and then again as a sodium ion with no chain ID.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>If you don’t care specifically about the waters or ions (or both), one thing you could try is to open the file in Chimera as a regular multi-model PDB (rather than as a trajectory), and then delete the waters and/ or ions (i.e. ‘del solvent’ and/or ‘del ions’), and then save the PDB as a single file again. Then that file should be able to be opened as a trajectory.</div><div class=""><br class=""></div><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 class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 15, 2018, at 7:24 PM, ChuHui Fu <<a href="mailto:cfu@haverford.edu" class="">cfu@haverford.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi all, <br class=""></div><div class=""><br class=""></div><div class="">When I was trying to use MD Movie option on the attached pdb trajectory file, chimera kept telling me that there were missing residues. <br class=""></div><div class=""><br class=""></div><div class="">"Chimera Error</div><div class="">Residue 3864.het not in first model on line 126754 of <br class=""></div><div class="">/homes/cfu/model1_sep_475.B_md_traj_system.pdb"</div><div class=""><br class=""></div><div class=""><div class=""><div class="">But I checked that the number of atoms in each one of the pdb files and there didn't seem to be any missing. Then I separated the trajectory files and use vimdiff to compare the models pairwise, but doesn't seem like there are different residues, (unless I missed them). <br class=""></div><div class=""><br class=""></div><div class="">Can anyone suggest what I might have done wrong? <br class=""></div><div class=""><br class=""></div><div class=""><div class="gmail_chip gmail_drive_chip" style="width:396px;height:18px;max-height:18px;background-color:rgb(245,245,245);padding:5px;font-family:arial;font-weight:bold;border:1px solid rgb(221,221,221);line-height:1"><a href="https://drive.google.com/a/haverford.edu/file/d/1w82K6a2FfLDzphcn6Jj2VwCjokFbXzqu/view?usp=drive_web" target="_blank" style="display:inline-block;max-width:366px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0;border:none" class=""><img style="vertical-align: bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png" class=""> <span dir="ltr" style="color:rgb(17,85,204);text-decoration:none;vertical-align:bottom" class="">model1_sep_475.B_md_traj_system.pdb</span></a><img src="x-msg://ssl.gstatic.com/ui/v1/icons/common/x_8px.png" style="opacity: 0.55; cursor: pointer; float: right; position: relative; top: -1px; display: none;" class=""></div><br class=""></div><div class="">Thanks!!<br class=""></div><div class=""><br class=""></div><div class="">-- <br class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">ChuHui Fu </div><div class="">B.S.Candidate in Chemistry <br class=""></div><div class=""><span style="font-size:12.8px" class="">Haverford College, Class of 2019</span><br class=""></div><div class=""><a href="mailto:cfu@haverford.edu" target="_blank" class="">cfu@haverford.edu</a></div><div class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div>
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