<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><br class=""><blockquote type="cite" class="">On Jan 13, 2022, at 10:54 AM, Joshi, Keya <<a href="mailto:keyajoshi1996@ku.edu" class="">keyajoshi1996@ku.edu</a>> wrote:<br class=""><br class="">Hello Prof. Meng,<br class=""> Hope you are doing well and staying safe. My name is Keya Joshi. I am a second year PhD student in the department of Computational Biology at the University of Kansas. I am trying to use Chimera to protonate Histidine residue 816 in chain B. But I have no idea about how to do this using Chimera. <br class=""> Can you please help me with this?<br class=""><br class="">With Regards<br class="">Keya Joshi<br class=""></blockquote><br class=""><div class="">Hi Keya,</div><div class="">I hope you are well, too!</div><div class=""><br class=""></div><div class="">(CC-ing the <a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> address which is recommended for asking Chimera questions unless you are sending data that needs to remain private)</div><div class=""><br class=""></div><div class="">In the structure that you sent, histidine 816 in chain B is already protonated (already has hydrogens). However, it is protonated to the neutral state. Maybe you meant you wanted one more hydrogen to make it the positively charged state.</div><div class=""><br class=""></div><div class="">Two ideas:</div><div class="">(1) You can just use the AddH tool (menu: Tools... Structure Editing... AddH) or "addh" command to add hydrogens to the whole protein. See help for information about the options:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html</a>></div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html</a>></div><div class=""><br class=""></div><div class="">On the PDB file that you sent, the default options of AddH (= simply using command "addh" without any other options) do add a hydrogen to 816 in chain B to put it in the positively charged state, but it also adds lots of other hydrogens including on carbons and on all of the other residues. I don't know if that is a problem for you, or whether it is an improvement on the original structure. Of course you can delete some hydrogens afterward, but it depends what you want.</div><div class=""><br class=""></div><div class="">(2) To just add one hydrogen to that sidechain nitrogen, instead use Build Structure (menu: Tools... Structure Editing... Build Structure), and in that tool change from "Start Structure" to "Modify Structure". Select (Ctrl-click on) the nitrogen of His 816 that needs the hydrogen. Selection is shown with a green outline on that atom. Then in the tool, you want that selected atom to be N (stay the same element) but with 3 bonds and trigonal geometry as shown in the screenshot. Also as shown in the screenshot, choose the option to leave the residue name unchanged. Then click Apply to add that one hydrogen.</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="28B06DDB-5997-4DD9-AA8C-1600A8B18553" width="640" height="462" src="cid:90FB8695-6BC9-4D8A-99A6-35123CCAEBC5" class=""></div><div class=""><br class=""></div><div class="">... after I click Apply it looks like this:</div><div class=""><img apple-inline="yes" id="63D81CA8-97CC-47AC-B15C-4C724AADE982" width="640" height="461" src="cid:4BC982BD-EC3C-45F1-81B8-81F06084AF42" class=""></div><div class=""><br class=""></div><div class="">about selection:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html</a>></div><div class=""><br class=""></div><div class="">Build Structure tool:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html</a>></div><div class=""><br class=""></div><div class="">You can find Chimera features using Chimera menu: Help... Search Documentation, e.g. to search for "hydrogens" or "building"</div><div class=""><br class=""></div><div class="">Our newer program ChimeraX also has an "addh" command.</div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br 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=""><br class=""></div></body></html>