<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hmmm, oops. :-). Tomorrow's daily build will not put out SEQRES records for chains where it doesn't know the complete sequence.<div class=""><br class=""></div><div class="">--Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 11, 2023, at 2:41 PM, Jonathan Jih <<a href="mailto:jihmailed@gmail.com" class="">jihmailed@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">That makes a lot of sense - thanks for the explanation Eric!<div class=""><br class=""></div><div class="">Is there perhaps a way to disable automatic SEQRES generation when saving pdbs within ChimeraX? I noticed that when I load a pdb with no SEQRES info (thereby having missing structure pseudobonds display correctly), upon resaving that pdb, new SEQRES info is automatically generated causing the issue to rear again. I then have to go back and manually delete SEQRES for each one of the pdbs I generate.</div><div class=""><br class=""></div><div class="">Appreciate all the help. </div><div class=""><br class=""></div><div class="">Jonathan</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jan 11, 2023 at 2:37 PM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class="">Just for the curious bystanders, the problem is that the SEQRES records -- which are supposed to supply the complete sequence of the polymer -- indicated that the far-apart residues were consecutive in sequence. ChimeraX therefore suppressed the display of the missing-structure pseudobond.<div class=""><br class=""></div><div class="">--Eric<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jan 11, 2023, at 12:35 PM, Jonathan Jih via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class="">Hi Eric,<div class=""><br class=""></div><div class="">I can confirm that opening 1www does display pseudobonds properly. I played around with my pdb files, and it seems if the issue can be resolved if I either: 1) delete or modify a residue in ChimeraX and then resave the pdb, or 2) if I fully delete the SEQRES header of each pdb file.</div><div class=""><br class=""></div><div class="">In any case, I'll send you separately two test pdbs I've created. Thanks for the prompt response! </div><div class=""><br class=""></div><div class="">Jonathan</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jan 11, 2023 at 10:33 AM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" target="_blank" class="">pett@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="">Hi Jonathan,<div class=""><span style="white-space:pre-wrap" class=""> </span>So if you open a structure such as 1www, are the missing-structure pseudobonds displayed? If they are, then I would need access to one of your PDB files (or part of of one) that demonstrates the problem -- which you could send to me directly.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span>Eric Pettersen</div><div class=""><span style="white-space:pre-wrap" class=""> </span>UCSF Computer Graphics Lab</div></div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jan 11, 2023, at 2:35 AM, Jonathan Jih via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Hello ChimeraX team,<div class=""><br class=""></div><div class="">I'm having quite a bit of trouble displaying missing structure dashed lines when my models are shown in cartoon mode. This is despite the "missing structure" sub-model box being ticked in the model panel.</div><div class=""><br class=""></div><div class="">I recall finding a workaround for this nearly a year ago on ChimeraX 1.3, but I cannot for the life of me remember how I did so (now using ChimeraX 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever workaround I applied back then display the missing structure dashed lines properly in 1.5. However, opening the exact same pdb files from those older sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode appears fine.</div><div class=""><br class=""></div><div class="">I also found this thread (<a href="https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html" target="_blank" class="">https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html</a>), which seems to indicate the issue has been fixed, so not sure if I'm just doing something wrong? </div><div class=""><br class=""></div><div class="">My OS is Windows 11 if that matters. Thanks in advance for the help!</div><div class=""><br class=""></div><div class="">Jonathan</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">-- <br class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="">Biochemistry, Biophysics, and Structural Biology (BBSB)</div><div class="">Molecular Biology Institute, University of California, Los Angeles</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div style="color:rgb(136,136,136);font-size:12.8px" class=""></div></div></div></div></div></div></div>
_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" target="_blank" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></div></blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="">Biochemistry, Biophysics, and Structural Biology (BBSB)</div><div class="">Molecular Biology Institute, University of California, Los Angeles</div><div class=""><br class=""></div><div class=""><div style="color:rgb(136,136,136);font-size:12.8px" class=""></div></div></div></div></div></div>
_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" target="_blank" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></div></blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div dir="ltr" class=""><div class="">Biochemistry, Biophysics, and Structural Biology (BBSB)</div><div class="">Molecular Biology Institute, University of California, Los Angeles</div><div class=""><br class=""></div><div class=""><a href="http://www.denovomods.com/" style="font-size:12.8px;color:rgb(17,85,204)" target="_blank" class="">De Novo Modeling Solutions</a><br class=""></div><div class=""><div style="color:rgb(136,136,136);font-size:12.8px" class=""><div style="font-size:12.8px" class=""><a href="mailto:projects@denovomods.com" style="color:rgb(17,85,204)" target="_blank" class="">projects@denovomods.com</a> | <a href="tel:(831)%20419-7729" value="+18314197729" style="color:rgb(17,85,204)" target="_blank" class="">(831) 419-7729<br class=""></a></div></div></div></div></div></div>
</div></blockquote></div><br class=""></div></body></html>