<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 Boris,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You can put the script wherever you want. You just need to run it (by opening it with File→Open or the “open” command) after running ‘addcharge’ on your structures. If you do this a lot, you might want to consult the documentation for the ‘alias command (<i class="">i.e.</i> “help alias”) to make the process more convenient.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera will basically never consider the cysteine sulphur to be deprotonated by default. Therefore, you never get the Amber residue type CYM. You would have to force Chimera to consider the sulphur to be deprotonated by changing its IDATM type to ‘S3-‘ (negatively charged <i class="">sp3</i> sulphur). You would do this (before adding hydrogens!) by selecting the sulphurs you want to change and then using this command:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>setattr a idatmType S3- sel</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-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>
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<div><br class=""><blockquote type="cite" class=""><div class="">On Sep 4, 2018, at 1:22 AM, Boris TOUZEAU <<a href="mailto:boris.touzeau@gmail.com" class="">boris.touzeau@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi,<br class=""></div><div class="">I have another issue with the script, correct me if I am wrong but it goes inside my own chimera names residues depositery and fetch the name right ? However it fails to fetch the cystein residue CYM. Is chimera name library up to date ?<br class=""><br class=""></div><div class="">Best wishes,<br class=""><br class=""></div><div class=""> Boris TOUZEAU<br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="">Le mar. 28 août 2018 à 04:59, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> a écrit :<br class=""></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space" class="">Hi Boris,<div class=""><span class="m_7458391256837499999Apple-tab-span" style="white-space:pre-wrap"> </span>Well, not directly. If you run the AddCharge tool (or ‘addcharge’ command), which will in turn add hydrogens if any are missing, then the “Amber name” of the residue is computed and put into the ‘amberName’ attribute of each residue. So, if you then run the Python script below (simply by opening it with File→Open or the “open” command), then the regular name of the residue will be overwritten with the amberName attribute and if you then save a PDB file, the residue names will use the Amber convention.</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; word-wrap: break-word;" class=""><div class=""><span class="m_7458391256837499999Apple-tab-span" style="white-space:pre-wrap"> </span>Eric Pettersen</div><div class=""><span class="m_7458391256837499999Apple-tab-span" style="white-space:pre-wrap"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div><div class=""></div></div></div></div></div><div style="word-wrap:break-word;line-break:after-white-space" class=""><div class=""><div class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;" class=""><div class=""></div></div><br class="m_7458391256837499999Apple-interchange-newline">
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On Aug 27, 2018, at 2:00 AM, Boris TOUZEAU <<a href="mailto:boris.touzeau@gmail.com" target="_blank" class="">boris.touzeau@gmail.com</a>> wrote:</div><br class="m_7458391256837499999Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Hi,<br class=""><br class=""></div>I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei. <br class=""><br class=""></div>I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues.<br class=""><br class=""></div>Best wishes,<br class=""><br class=""></div> Boris TOUZEAU<br class=""></div>
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