<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 Mike, <div class=""><br class=""></div><div class="">I believe PYMOL draws bonds where atoms are within a certain distance (I think it is in pymol source /pymol/layer2/ Atominfo.cpp) or where there is explicit record found in the cif file, hence you see connectivity.</div><div class=""><br class=""></div><div class="">According to the CHIMERA website (<a href="https://www.cgl.ucsf.edu/chimera/data/mmcif-oct2013/mmcif.html" class="">https://www.cgl.ucsf.edu/chimera/data/mmcif-oct2013/mmcif.html</a>), CHIMERA has a dictionary of standard bond template for 265 residues and uses that to create your bonds. Perhaps your converted mmCIF has non-standard residues? </div><div class=""><br class=""></div><div class="">In any case, I think RCSB requires coordinates and structure factor file only (but this could have changed in recent years). My personal opinion is that I wouldn’t worry too much about bond connectivity, but that your R statistics for your structure is reasonable for your resolution. </div><div class=""><br class=""></div><div class="">Hope this helps, </div><div class="">Dave</div><div><blockquote type="cite" class=""><div class="">On Apr 8, 2016, at 10:49 AM, Michael Blaisse <<a href="mailto:mblaisse@berkeley.edu" class="">mblaisse@berkeley.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello,<div class=""><br class=""><div class="">I'm solving a crystal structure and as I'm preparing to submit the final structure to PDB, I used the PDB_Extract tool to convert my final refined .pdb to an mmCIF file as per the request of PDB. After I do this, however, I noticed that if I open the CIF file in Chimera, it does not have any connectivity between the residues. This does not appear to be a problem in PyMOL. </div></div><div class=""><br class=""></div><div class="">Less importantly, I also had a question about the Sequence view in Chimera. I have a break in my chain due to unmodelled residues, and I noticed that if I float my cursor over a residue in the sequence, it shows the correct residue number at the bottom of the window, however the numbering at the side of the sequence view window is wrong after the break because it does not take the chain break into account.</div><div class=""><br class=""></div><div class="">I appreciate any advice/help people can offer.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Mike</div></div>
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