Dear Justin,<br><br>Thanks for your reply. There are not percentage of secondary structure in "scount.xvg".<br><span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps">The content</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">of the </span></span>"scount.xvg"<span id="result_box" class="short_text" lang="en"><span title="Alternatif çevirileri görmek için tıklayın" class="hps"> file</span> <span title="Alternatif çevirileri görmek için tıklayın" class="hps">are as the following:</span></span><br>
<br># This file was created Tue Jan 4 19:28:47 2011<br># by the following command:<br># do_dssp -s run.tpr -f run.xtc <br>#<br># do_dssp is part of G R O M A C S:<br>#<br># GROup of MAchos and Cynical Suckers<br>#<br>@ title "Secondary Structure"<br>
@ xaxis label "Time (ps)"<br>@ yaxis label "Number of Residues"<br>@TYPE xy<br>@ subtitle "Structure = A-Helix + B-Sheet + B-Bridge + Turn"<br>@ view 0.15, 0.15, 0.75, 0.85<br>@ legend on<br>
@ legend box on<br>@ legend loctype view<br>@ legend 0.78, 0.8<br>@ legend length 2<br>@ s0 legend "Structure"<br>@ s1 legend "Coil"<br>@ s2 legend "B-Sheet"<br>@ s3 legend "B-Bridge"<br>
@ s4 legend "Bend"<br>@ s5 legend "Turn"<br>@ s6 legend "A-Helix"<br>@ s7 legend "3-Helix"<br> 0 128 19 14 1 17 11 102 0<br> 0.2 131 19 14 1 14 14 102 0<br>
0.4 132 19 14 1 13 23 94 0<br> 0.6 130 19 14 1 15 12 103 0<br> 0.8 132 19 14 1 13 19 98 0<br> 1 130 21 14 1 13 28 87 0<br>
.................................................................<br><br><div class="gmail_quote">04 Ocak 2011 20:04 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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 class="im"><br>
<br>
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;">
Dear Justin,<br>
<br>
I am using the commands as the following.<br>
do_dssp -s run.tpr -f run.xtc<br>
xpm2ps -f ss.xpm -o ss.eps<br>
<br>
You said "Have a look at the other output file do_dssp gives you". which one should I look?<br>
<br>
</blockquote>
<br></div>
Well, there's another output file from do_dssp called "scount.xvg," which should be almost exactly what you need. See do_dssp -h for a description, then look at the file yourself.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks<br>
<br>
04 Ocak 2011 15:51 tarihinde Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> yazdı:<div><div>
</div><div class="h5"><br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
I get the residue versus time ( secondary structure graph) using<br>
do_dssp tool. I want to get the percentage value(alpha helix,<br>
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>
<br>
Have a look at the other output file do_dssp gives you.<br>
<br>
-Justin<br>
<br>
<br>
04 Ocak 2011 14:59 tarihinde Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>> yazdı:<br>
<br>
<br>
On 4/01/2011 11:38 PM, ahmet yıldırım wrote:<br>
<br>
Dear Mark,<br>
<br>
I will do by using the g_analyze tool but I do not know<br>
how to use it.<br>
<br>
<br>
There's a section in Appendix D of the manual for each tool,<br>
or you<br>
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<br>
specific analysis"<br>
<br>
Mark<br>
<br>
<br>
<br>
Thanks<br>
<br>
2011/1/4 Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>><br>
<br>
<br>
On 4/01/2011 8:33 PM, ahmet yıldırım wrote:<br>
<br>
Hi,<br>
<br>
How can I calculate the percentages (alpha helix,<br>
beta<br>
sheet, coil ...) of secondary structure?<br>
<br>
<br>
Look in manual section 7.4 for a suitable tool.<br>
<br>
Mark<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div><div></div><div class="h5"><br>
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</div></div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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