<br>This is the way to do it with Pymol for one frame:<br><br><a href="http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08154.html">http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08154.html</a><br>
<br>I guess with a little bit of python scripting you could read through all the frames of your trajectory. <br><br>Thomas<br><br><br><div class="gmail_quote">2011/1/4 ahmet yıldırım <span dir="ltr"><<a href="mailto:ahmedo047@gmail.com">ahmedo047@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">I get the residue versus time ( secondary structure graph) using do_dssp tool. I want to get the percentage value(alpha helix, beta
sheet, coil ...) of secondary structure. For example:<br><br>Secondary structure percentage (%):<br>Helix:51.6<br>B-sheet:0<br>Random coil:24.0<br>Turn:24.4<br><br><div class="gmail_quote">04 Ocak 2011 14:59 tarihinde Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> yazdı:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
<div text="#000000" bgcolor="#ffffff"><div>
On 4/01/2011 11:38 PM, ahmet yıldırım wrote:
<blockquote type="cite">Dear Mark,<br>
<br>
I will do by using the g_analyze tool but <span lang="en"><span title="Alternatif çevirileri
görmek için tıklayın">I do not know</span> <span title="Alternatif çevirileri görmek için tıklayın">how
to use it.<br>
</span></span></blockquote>
<br></div>
There's a section in Appendix D of the manual for each tool, or you
can use the -h argument to the tool to get the same information.<br>
<br>
Either way, you haven't got the right tool. Hint: it's a "protein
specific analysis"<br><font color="#888888">
<br>
Mark</font><div><br>
<br>
<blockquote type="cite"><span lang="en"><span title="Alternatif çevirileri görmek için tıklayın">
<br>
Thanks<br>
<br>
</span></span>
<div class="gmail_quote">2011/1/4 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div>On 4/01/2011 8:33 PM, ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<br>
How can I calculate the percentages (alpha helix, beta
sheet, coil ...) of secondary structure?<br>
</blockquote>
<br>
</div>
Look in manual section 7.4 for a suitable tool.<br>
<br>
Mark<br>
<font color="#888888">
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<br>
<br clear="all">
<br>
-- <br>
Ahmet YILDIRIM<br>
</blockquote>
<br>
</div></div>
<br></div></div>--<div class="im"><br>
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