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To answer your question regarding ISOLDE: yes, if you change the protonation state of an acid or histidine residue then it will be treated as (un)charged accordingly. If you just want to protonate a single acid, you could select the relevant oxygen and then
do ISOLDE/Model Building/Add Hydrogen. For a histidine, select any atom in the residue, then use the command "isolde mod his sel {ND|NE|both}" (or "isolde shorthand" once, then "ht {ND|NE|both}" from then on), where "ND", "NE" or "both" refer to the nitrogen(s)
to be protonated.</div>
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-- Tristan</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Voss Jonathan Mark via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
<b>Sent:</b> 23 March 2022 09:06<br>
<b>To:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> [chimerax-users] addh</font>
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<p>Hello,</p>
<p><br>
</p>
<p>I would like to protonate ASP, GLU, and HIS side chains throughout a model. I'm a little confused about the syntax of the
<span>useAspName, <span style="font-family:Calibri,Helvetica,sans-serif,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">useGluName, etc. option. I've looked around but haven't
found any examples. Could you provide one?</span></span></p>
<p><span><span style="font-family:Calibri,Helvetica,sans-serif,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><br>
</span></span></p>
<p>Furthermore, once a side chain is protonated, will ISOLDE recognize that site as being charged? Or does this need to be specified somehow?</p>
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<p>Best</p>
<p>-Jon</p>
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