<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hello,<div class="">Just look carefully at one protein chain first. Distances are measured between atoms. So you have to first figure out what atoms are at the C-term and N-term that you want to use for the measurement. </div><div class=""><br class=""></div><div class="">(1) open structure, show all atoms (e.g. menu: Presets... Interactive 2 (all atoms))</div><div class=""><br class=""></div><div class="">(2) if you don't already know their residue numbers, find N-term and C-term. There are many ways to do it. One way is to show Sequence (menu: Favorites... Sequence, choose the chain that you are looking at, show its sequence), and then in the sequence window:</div><div class=""><br class=""></div><div class="">- draw a box to highlight the first residue in the chain (green box in sequence will be shown as selection on 3D structure)</div><div class="">- zoom in on and label those atoms, e.g. commands</div><div class=""><br class=""></div><div class="">focus sel</div><div class="">label sel</div><div class="">rlabel sel</div><div class=""><br class=""></div><div class="">That is just the N-terminus, decide which atom you want to use for the measurement and write it down. E.g. my protein has these atoms at the N-terminus so I could decide to use atom "N" of residue 1 in chain A.</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="A5B49A73-B3F1-402C-9087-8FA699425238" width="302" height="208" src="cid:A8269BC8-89B6-4465-952A-2252E6AC5315" class=""></div><div class=""><br class=""></div><div class="">Then repeat to find and label the C-terminal residue (select in sequence window the last residue in the structure, focus sel, etc.).</div><div class=""><br class=""></div><div class="">(3) Then you have a list of the two atoms you want to use, and can use a command to add the distance, for example:</div><div class=""><br class=""></div><div class="">distance :1.A@N :309.A@C</div><div class=""><br class=""></div><div class="">...meaning measure distance between residue 1 in chain A atom N, and residue 309 in chain A atom C.</div><div class=""><br class=""></div><div class="">There are other ways too, e.g. Ctrl-click first atom in 3D view, then find 2nd atom and Ctrl-doubleclick, and then choose Distance from the context menu that pops up. See examples in tutorial, and the Distance help:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html</a>></div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances" class="">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances</a>></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine</div><div class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <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=""><br class=""></div><br class=""><blockquote type="cite" class="">On Feb 3, 2023, at 6:40 AM, squirrel via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Dear Ms/Mr：<br class="">Thanks for your wonderful tool! <br class="">I meet a problem recently. Every proteins have N-terminations and C-terminations, and I want to measure the distance between all proteins at each other's N-C, N-N, and C-C terminals by using UCSF Chimera. But there are too many proteins for me to start.I've read Chimera's tutorials and searched my questions online. But I didn't find the answer I needed.Can you please give me some guidance or tips？ <br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></blockquote><br class=""></div></body></html>