<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="">Hi Daniel,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera learns that non-standard residues are modified forms of regular amino/nucleic acids from the MODRES records in PDB files. If you added MODRES records for your residues to your input file, the sequence would show S/T instead of X. The format for a MODRES record is documented here:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#MODRES" class="">http://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#MODRES</a></div><div class=""><br class=""></div><div class="">You could crib MODRES records for your residues from 1vrv (SEP) and 6ar2 (TPO). You would have to edit the chain ID and sequence number fields of those records.</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">On Feb 5, 2020, at 7:34 AM, Daniel Hilger <<a href="mailto:daniel.hilger@pharmazie.uni-marburg.de" class="">daniel.hilger@pharmazie.uni-marburg.de</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=""><span style="caret-color: rgb(0, 0, 0);" class="">Hi,</span><div class="" style="caret-color: rgb(0, 0, 0);"><br class=""></div><div class="" style="caret-color: rgb(0, 0, 0);">I modeled two phosphorylated residues in my structure. The primary sequence window in Chimera, however, is only showing a “X” at those positions. Is there a possibility to change that to the original amino acid (S or T) or to show them as SEP or TPO in the sequence window?</div><div class="" style="caret-color: rgb(0, 0, 0);">Thanks,</div><span style="caret-color: rgb(0, 0, 0);" class="">Daniel</span><div class=""><span style="font-size: 14px; caret-color: rgb(0, 0, 0);" class=""><br class=""></span></div><div class=""><span style="font-size: 14px; caret-color: rgb(0, 0, 0);" class=""><br class=""></span></div><div class=""><span style="font-size: 14px; caret-color: rgb(0, 0, 0);" class="">Daniel Hilger, Dr.</span><br class=""><div class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><span style="font-size: 11px;" class="">Group leader </span><br style="font-size: 11px;" class=""><span style="font-size: 11px;" class="">Philipps-University Marburg</span><br style="font-size: 11px;" class=""><span style="font-size: 11px;" class="">Marbacher Weg 6</span><br style="font-size: 11px;" class=""><span style="font-size: 11px;" class="">35032 Marburg</span><br style="font-size: 11px;" class=""><span style="font-size: 11px;" class="">Germany</span><br style="font-size: 11px;" class=""><span style="font-size: 11px;" class=""><a href="mailto:daniel.hilger@pharmazie.uni-marburg.de" class="">daniel.hilger@pharmazie.uni-marburg.de</a></span><br style="font-size: 11px;" class=""><span style="font-size: 11px;" class="">Phone: +49 6421 28 25930</span></div><div class=""><br class=""></div></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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<br class=""></div></div>_______________________________________________<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="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>