<html xmlns:v="urn:schemas-microsoft-com:vml" 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)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:Mangal;
panose-1:2 4 5 3 5 2 3 3 2 2;}
@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;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body lang="EN-AU" link="blue" vlink="#954F72" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal">Hi, </p>
<p class="MsoNormal">First of all thank you so much for making such a wonderful tool and sharing it freely with scientific community.</p>
<p class="MsoNormal">I have been using chimera for sometime now and performed docking analysis using autodock vina.
</p>
<p class="MsoNormal">I recently come across a problem.</p>
<p class="MsoNormal">After exporting pdb file with desired docking pose, I tried to run protein ligand interaction analysis on
<a href="https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index">PLIP</a> server. But ligand in my file does not get recognised for analysis.
</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I opened pdb file in a text editor and upon looking care fully I see chimera saves receptor and ligand as separate model like this</p>
<div>
<div>
<p class="MsoNormal"><i>ATOM 7453 HD2 PRO A 462 15.986 11.983 20.450 1.00 0.00 H</i><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><i>ATOM 7454 HD3 PRO A 462 16.532 10.334 20.885 1.00 0.00 H</i><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><i>ENDMDL</i><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><i>MODEL 2</i><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><i>HETATM 1 S1 CGT A 1 9.051 5.106 43.099 1.00 0.00 S</i><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><i>HETATM 2 C6 CGT A 1 8.150 3.680 42.370 1.00 0.00 C</i><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">After comparing it with the pdb file from pbd database I removed “ENDMDL” and “MODEL 2” and re-ran the PLIP analysis. This time it works but PLIP also mentions that –
</p>
<p class="MsoNormal"><img border="0" width="276" height="122" style="width:2.875in;height:1.2708in" id="Picture_x0020_3" src="cid:image001.png@01D7103D.5D0AB030"></p>
<p class="MsoNormal">Analysis went well but the .pse file that I get from PLIP server does not allow me to show ligand in stick format in Pymol software.
</p>
<p class="MsoNormal">I suspect this is due to the original pdb file format. I also noticed that pdb file when opened in pymol shows ligand and receptor as different states which is not correct (if I am right).</p>
<p class="MsoNormal">I have attached both original pdb file that I saved from Chimera-autodock vina and pse file from PLIP analysis.</p>
<p class="MsoNormal">May I request to help me resolve this issue?</p>
<p class="MsoNormal">Please let me know if you need any further information or clarification.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for your time and support</p>
<p class="MsoNormal"><a name="_MailAutoSig"><b><span style="color:#7030A0">Amol<o:p></o:p></span></b></a></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailAutoSig"><b><span style="color:#7030A0"><o:p> </o:p></span></b></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailAutoSig"><b><span style="color:#7030A0">---------------------------------------------------------------------------------------------------------------------------------------------------------<o:p></o:p></span></b></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailAutoSig"><b><span style="font-size:14.0pt;color:#7030A0">Dr Amol Bharat Ghodke | Post-Doctoral Research Fellow<o:p></o:p></span></b></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailAutoSig"><b><span style="font-size:10.0pt;color:#7030A0"><o:p> </o:p></span></b></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailAutoSig"><b><span style="color:#7030A0">Queensland Alliance for Agriculture and Food Innovation<o:p></o:p></span></b></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailAutoSig"><span style="color:#7030A0">Level 3, Queensland Bioscience Precinct [#80]<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailAutoSig"><span style="color:#7030A0">Room 3.318, 306 Carmody Rd, St Lucia
<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailAutoSig"><span style="color:#7030A0">The University of Queensland<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailAutoSig"><span style="color:#7030A0">St Lucia, Brisbane Qld 4072, AU<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailAutoSig"><span style="color:#7030A0">E.
</span></span><span style="mso-bookmark:_MailAutoSig"></span><a href="mailto:a.ghodke@uq.edu.au"><span style="mso-bookmark:_MailAutoSig"><span style="color:#7030A0">a.ghodke@uq.edu.au</span></span><span style="mso-bookmark:_MailAutoSig"></span></a><span style="mso-bookmark:_MailAutoSig"></span>
<span style="color:#7030A0"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</body>
</html>