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On 5/01/2011 12:35 AM, ahmet yıldırım wrote:
<blockquote
cite="mid:AANLkTimSL7WkfFRx07uozFEXH412xG3VHGbt_1ZLz_cq@mail.gmail.com"
type="cite">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. </blockquote>
<br>
Please say this in the *first* email. Giving a full description of
what you have done and what you got as output and why it isn't yet
suitable runs a much lower risk of wasting the time of everyone who
reads your email and has to guess what help you want. See
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support">http://www.gromacs.org/Support</a> - had you followed these steps you'd
have probably had an answer from Justin in one email.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTimSL7WkfFRx07uozFEXH412xG3VHGbt_1ZLz_cq@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">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 text="#000000" bgcolor="#ffffff">
<div class="im"> 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 class="im"><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 moz-do-not-send="true"
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"> -- <br>
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</div>
<br>
<br clear="all">
<br>
-- <br>
Ahmet YILDIRIM<br>
</blockquote>
<br>
</div>
</div>
<br>
--<br>
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</blockquote>
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<br>
<br clear="all">
<br>
-- <br>
Ahmet YILDIRIM<br>
</blockquote>
<br>
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