<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=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@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:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0in;
margin-right:0in;
margin-bottom:0in;
margin-left:.5in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:194000071;
mso-list-type:hybrid;
mso-list-template-ids:-1676876762 67698705 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l0:level1
{mso-level-text:"%1\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:.75in;
text-indent:-.25in;}
@list l0:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:1.25in;
text-indent:-.25in;}
@list l0:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
margin-left:1.75in;
text-indent:-9.0pt;}
@list l0:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:2.25in;
text-indent:-.25in;}
@list l0:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:2.75in;
text-indent:-.25in;}
@list l0:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
margin-left:3.25in;
text-indent:-9.0pt;}
@list l0:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:3.75in;
text-indent:-.25in;}
@list l0:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:4.25in;
text-indent:-.25in;}
@list l0:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
margin-left:4.75in;
text-indent:-9.0pt;}
@list l1
{mso-list-id:837647489;
mso-list-type:hybrid;
mso-list-template-ids:701134864 67698705 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l1:level1
{mso-level-text:"%1\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l1:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l1:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
ol
{margin-bottom:0in;}
ul
{margin-bottom:0in;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal">Hi, <o:p></o:p></p>
<p class="MsoNormal"> In making surfaces around ligands and making them transparent, I ran into some problems:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Using open/fetch 3NHA I have a molecule in front of me with ADP Mg bound.
<o:p></o:p></p>
<p class="MsoNormal">Creating a surface around ADP is easy but it won’t cover Mg at all. It seems that single ions like Mg and also single water molecules don’t get surfaces around them. Is this because of default vdW values that need to be manually adjusted
?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Let’s say I have a surface around ADP and want to make it transparent, I thought
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Transparency 50,s #0 <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Should work but it did not. There are some work arounds using transparent colors through the use of colordef.
<o:p></o:p></p>
<p class="MsoNormal">However, I had planned to color the surface by atom and used
<o:p></o:p></p>
<p class="MsoNormal"> scolor #0 zone #0 <o:p></o:p></p>
<p class="MsoNormal">which worked but I could not get it transparent with transparency statements. However, I can make atoms transparent then use
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">scolor #0 zone #0 #which makes the surface also transparent and hides the ball-and-stick model.<o:p></o:p></p>
<p class="MsoNormal">To make it show up I can use transparency 0,a #0 and again the stick model appears under the transparent surface.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Is there a simpler way ? A way that can be applied to other surfaces that were for instance colored with say potential, hydrophobicity, bfactor key etc ?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks<o:p></o:p></p>
<p class="MsoNormal">Lothar<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoListParagraph"><o:p> </o:p></p>
</div>
</body>
</html>