<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
</head>
<body ocsi="0" fpstyle="1" bgcolor="#ffffff">
<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 13px;">
<div style="">I really do not know how to get those beta-sheet structures out,<br>
or maybe by which ways?<br>
<br>
Any clues are warmly welcomed and appreciated.<br>
<br>
lina <br>
</div>
<div style="font-family: Times New Roman; color: rgb(0, 0, 0); font-size: 16px;">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF804562"><font color="#000000" face="Tahoma" size="2"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of Mark Abraham [Mark.Abraham@anu.edu.au]<br>
<b>Sent:</b> Sunday, November 21, 2010 11:58 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] find the relevant structure out<br>
</font><br>
</div>
<div></div>
<div>On 21/11/2010 11:43 PM, #ZHAO LINA# wrote:
<blockquote type="cite"><style id="owaParaStyle" type="text/css">
<!--
p
{margin-top:0;
margin-bottom:0}
-->
BODY {direction: ltr;font-family: Tahoma;color: #000000;font-size: 13px;}P {margin-top:0;margin-bottom:0;}</style>
<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 13px;">
<div style="">Hi,<br>
<br>
I had done 10ns simulation, <br>
<br>
by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix.<br>
<br>
there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets.<br>
<br>
After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive.<br>
<br>
Or maybe some parts I understand wrong.<br>
<br>
Thanks for any advice and if I am wrong please let me know,<br>
</div>
</div>
</blockquote>
<br>
We've really no idea of the detail of what you've done, so can't guess. Just about anything could be the problem - all the way from "you are looking at the wrong files", to "pymol's definition of a beta sheet doesn't agree with dssp".<br>
<br>
If you can't report the command lines you used easily, then your method was not reproducible enough, or not recorded well enough :-)<br>
<br>
Mark<br>
</div>
</div>
</div>
</body>
</html>