<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Forgot to mention that one easy way to delete all hydrogens is with the command “del H” (Favorites→Command Line).<div class=""><br class=""></div><div class="">—Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 26, 2018, at 11:13 AM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Renee,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>For standard residues, Chimera simply looks up the Amber atom type and partial charge (both needed for minimization) in a table based on the atom’s name. Obviously for this to work the atom needs to have the appropriate PDB-standard name. There is no ‘H1’ atom in standard PDB GLN residues.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Typically the easiest way to remedy this, since you are about to minimize the structure anyway, is to delete the existing hydrogens and let Chimera add them back during the minimization prep — which will ensure they have the correct names in most cases. The one case I can think of where that doesn’t work is if there are <i class="">backbone</i> heavy atoms missing in a residue. In that situation it may be best to delete the residue entirely.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jul 25, 2018, at 4:03 PM, Renee Arias <<a href="mailto:rarias72@gmail.com" class="">rarias72@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello all,<div class=""><br class=""></div><div class="">I am having a problem with the minimizing structure function in Chimera. I am just trying to change a single residue on a very small protein (88 residues), but I keep getting the error: No MMTK name for atom "H1" in standard residue "GLN". Previous message boards seem to just point to bug fixes in Chimera, but I am running the newest version available for Windows 10. </div><div class=""><br class=""></div><div class="">I would appreciate any help!</div><div class=""><br class=""></div><div class="">Thanks so much,</div><div class=""><br class=""></div><div class="">Renee</div></div>
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