<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
mso-ligatures:standardcontextual;
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0cm;
margin-right:0cm;
margin-bottom:0cm;
margin-left:36.0pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
mso-ligatures:standardcontextual;
mso-fareast-language:EN-US;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:267742920;
mso-list-type:hybrid;
mso-list-template-ids:-1634854480 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
@list l0:level1
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l1
{mso-list-id:1056583248;
mso-list-type:hybrid;
mso-list-template-ids:-1899335362 -1302970782 67895299 67895301 67895297 67895299 67895301 67895297 67895299 67895301;}
@list l1:level1
{mso-level-number-format:bullet;
mso-level-text:\F0D8 ;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Wingdings;
mso-fareast-font-family:Calibri;
mso-bidi-font-family:"Times New Roman";}
@list l1:level2
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l1:level3
{mso-level-number-format:bullet;
mso-level-text:\F0A7 ;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Wingdings;}
@list l1:level4
{mso-level-number-format:bullet;
mso-level-text:\F0B7 ;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
@list l1:level5
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l1:level6
{mso-level-number-format:bullet;
mso-level-text:\F0A7 ;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Wingdings;}
@list l1:level7
{mso-level-number-format:bullet;
mso-level-text:\F0B7 ;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
@list l1:level8
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l1:level9
{mso-level-number-format:bullet;
mso-level-text:\F0A7 ;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Wingdings;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style>
</head>
<body lang="FR" link="#0563C1" vlink="#954F72" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal">Hey Phil and Rohan,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">Thank you for your replies. I have only 2 copies of MLY.cif in the computer, one is in $CCP4/lib/data/monomers/m, the other one is in Coot’s directory under $CCP4, and they are identical. So I guess Buster is taking the
one from $CCP4, right?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If that’s correct, then yes, it is already as peptide:<o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US">MLY MLY N-DIMETHYL-LYSINE peptide 30 12 .<o:p></o:p></span></i></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<ul style="margin-top:0cm" type="disc">
<li class="MsoListParagraph" style="margin-left:0cm;mso-list:l1 level1 lfo2"><span lang="EN-US">Which is curious because, also for M3L for which the TER line is not added, Buster will always convert them to HETATM, even if you manually edit the pdb file.<o:p></o:p></span></li></ul>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">In Coot, the peptide bonds around the newly added MLY look OK, but I created the LINKs as suggested by Rohan anyways:<o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-US">LINK N MLY A 189 C THR A 188 1555 1555 <o:p></o:p></span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">LINK C MLY A 189 N LYS A 190 1555 1555 <o:p></o:p></span></i></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">But when Buster takes it up, it is still creating the TER line at aa 188… Even if I tell it
<i>Pdb2Tnt_RunAdjustLNNN=yes</i><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I believe this is something within the Buster/TNT/Gelly code, but my skills are not that developed to find where exactly… I wish there was a keyword like CreateTERLineBeforeSpecialResidue=no …<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-ligatures:none;mso-fareast-language:FR">Anyways, for the moment I using a workaround that I’m describing for records, for when other people face the same issue:<o:p></o:p></span></p>
<ol style="margin-top:0cm" start="1" type="1">
<li class="MsoListParagraph" style="color:black;margin-left:0cm;mso-list:l0 level1 lfo1">
<span lang="EN-US" style="mso-ligatures:none;mso-fareast-language:FR">Modify the refine.pdb: remove the TER line before the special amino acid;<o:p></o:p></span></li><li class="MsoListParagraph" style="color:black;margin-left:0cm;mso-list:l0 level1 lfo1">
<span lang="EN-US" style="mso-ligatures:none;mso-fareast-language:FR">Convert it to mmcif (for instance with
<a href="https://mmcif.pdbj.org/converter/">https://mmcif.pdbj.org/converter/</a></span><span lang="EN-US" style="color:windowtext;mso-ligatures:none;mso-fareast-language:FR"> );</span><span lang="EN-US" style="mso-ligatures:none;mso-fareast-language:FR"><o:p></o:p></span></li><li class="MsoListParagraph" style="color:black;margin-left:0cm;mso-list:l0 level1 lfo1">
<span lang="EN-US" style="mso-ligatures:none;mso-fareast-language:FR">Download the resulting mmcif file and submit that to Validate.<o:p></o:p></span></li></ol>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-ligatures:none;mso-fareast-language:FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-ligatures:none;mso-fareast-language:FR">This is much easier (at least to me) than modifying directly the BUSTER_model.cif, which requires many more changes (all those exclamation marks).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-ligatures:none;mso-fareast-language:FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-ligatures:none;mso-fareast-language:FR">Well, I’m still on the lookout for a real solution.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-ligatures:none;mso-fareast-language:FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-ligatures:none;mso-fareast-language:FR">All the best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-ligatures:none;mso-fareast-language:FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black;mso-ligatures:none;mso-fareast-language:FR">---------------------------------------------------<br>
Carlos KIKUTI, PhD<br>
UMR144 - CNRS - Institut Curie<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black;mso-ligatures:none;mso-fareast-language:FR">Pavillon Trouillet Rossignol <br>
26 Rue d’Ulm - 75005 Paris, France<br>
<a href="mailto:carlos.kikuti@curie.fr" title="mailto:carlos.kikuti@curie.fr"><span style="color:#0563C1">carlos.kikuti@curie.fr</span></a><o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</body>
</html>