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<div dir="ltr"><span><span style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;">Elaine</span></span><br clear="none"></div><div dir="ltr"><span><span style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;"><br clear="none"></span></span></div><div dir="ltr"><span><span style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;">Thank you for your help.</span></span></div><div dir="ltr"><span><span style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;"><br clear="none"></span></span></div><div dir="ltr"><span><span style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;">Yu</span></span></div><div dir="ltr"><span><span style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;"><br></span></span></div><div><br clear="none"></div>
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On Wednesday, September 22, 2021, 12:43:02 PM CDT, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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<div><div id="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><div>Dear Yu Zou,<div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">The PDB file does not explicitly say there is a chain break (there is no TER line) and there are no missing backbone atoms, so Chimera assumes that the consecutive residues in the same chain are bonded as normal. In other structures where there are missing residues, Chimera does show the dotted line (e.g. PDB structure 1maz).</div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"></div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">However, the bond between 127 and 128 is abnormally long (2.1 Angstroms). Probably Pymol detects the abnormally long bond and automatically makes it a chain break.</div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"></div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">I could tell that by hiding the ribbons (command: ~ribbon) and showing atoms (command: display) in Chimera, and then putting the cursor over the bond to show the pop-up with the bond length. You can remove the bond, e.g. command:</div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"></div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">~bond :127@c:128@n</div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"></div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">However, it still won't show the dotted line automatically because none of the atoms are missing. You could draw a dotted line by measuring the distance and then hiding the distance label, command:</div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"></div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">distance :127@c:128@n</div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"></div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">... and then menu: Tools... Structure Analysis... Distance, and use settings in that dialog to hide label, change color of dotted line, etc. See attached image.</div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"></div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">I hope this helps,</div><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">Elaine<br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">-----<br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">Elaine C. Meng, Ph.D. <br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">UCSF Chimera(X) team<br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">Department of Pharmaceutical Chemistry<br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">University of California, San Francisco<br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><img class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070" id="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070FFEC4927-E0F6-4A0D-8784-F65A0FBEE4BC" src="cid:1da6a9b7-33a4-2238-ffb1-7e45d9d00765@yahoo.com" style="width:480px;max-width:800px;" data-inlineimagemanipulating="true"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"></div><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><blockquote class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070" type="cite">On Sep 22, 2021, at 9:05 AM, Yu Zhou via Chimera-users <<a shape="rect" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070" href="mailto:chimera-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">Dear all,<br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">I am going through a Rosetta protein-protein docking tutorial using Chimera as the structure viewer. There is a chain break in the structure used for this tutorial (3gbn), which is caused by a severed connection between residue 127 and 128. Such chain break needs to be identified and fixed in a structural model before it could be used for Rosetta simulation. <br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">This chain break can be easily identified in Pymol as it is displayed as a dotted line. However, I cannot see this chain break in Chimera (and ChimeraX) as the segment is rendered as a beta-sheet. <br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">Is there a way to visualize such chain break in Chimera?<br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">Thanks,<br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">Yu Zhou<br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"><span><Pymol_chain break.jpg></span><span><Chimera_no chain break.jpg></span><span><3gbn_Ab.pdb></span>_______________________________________________<div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070yqt1667781987" id="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070yqtfd39986"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">Chimera-users mailing list: <a shape="rect" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070" href="mailto:Chimera-users@cgl.ucsf.edu" rel="nofollow" target="_blank">Chimera-users@cgl.ucsf.edu</a><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070">Manage subscription: <a shape="rect" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070" href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="nofollow" target="_blank">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"></div></blockquote><div class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070yqt1667781987" id="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070yqtfd32653"><br clear="none" class="ydp8ca114e6yiv9579575079ydpe22b4fc7yiv3905651070"></div></div></div></div></div>
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