ahmet yıldırım wrote:
Dear Justin,
Thanks for your reply. There are not percentage of secondary structure
in "scount.xvg".
I know that. But this is all the information you need. If you have a count of
how many residues are in a particular conformation over time, all you have to do
is divide by the number of total residues and you have your percentage.
Gromacs isn't going to do everything for you, but it quite often has the
capability to give you whatever raw data you need to properly manipulate.
-Justin
The content of the "scount.xvg" file are as the following:
# This file was created Tue Jan 4 19:28:47 2011
# by the following command:
# do_dssp -s run.tpr -f run.xtc
#
# do_dssp is part of G R O M A C S:
#
# GROup of MAchos and Cynical Suckers
#
@ title "Secondary Structure"
@ xaxis label "Time (ps)"
@ yaxis label "Number of Residues"
@TYPE xy
@ subtitle "Structure = A-Helix + B-Sheet + B-Bridge + Turn"
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "B-Sheet"
@ s3 legend "B-Bridge"
@ s4 legend "Bend"
@ s5 legend "Turn"
@ s6 legend "A-Helix"
@ s7 legend "3-Helix"
0 128 19 14 1 17 11 102 0
0.2 131 19 14 1 14 14 102 0
0.4 132 19 14 1 13 23 94 0
0.6 130 19 14 1 15 12 103 0
0.8 132 19 14 1 13 19 98 0
1 130 21 14 1 13 28 87 0
.................................................................
04 Ocak 2011 20:04 tarihinde Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> yazdı:
ahmet yıldırım wrote:
Dear Justin,
I am using the commands as the following.
do_dssp -s run.tpr -f run.xtc
xpm2ps -f ss.xpm -o ss.eps
You said "Have a look at the other output file do_dssp gives
you". which one should I look?
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.
-Justin
Thanks
04 Ocak 2011 15:51 tarihinde Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>> yazdı:
ahmet yıldırım wrote:
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:
Secondary structure percentage (%):
Helix:51.6
B-sheet:0
Random coil:24.0
Turn:24.4
Have a look at the other output file do_dssp gives you.
-Justin
04 Ocak 2011 14:59 tarihinde Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>> yazdı:
On 4/01/2011 11:38 PM, ahmet yıldırım wrote:
Dear Mark,
I will do by using the g_analyze tool but I do not
know
how to use it.
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.
Either way, you haven't got the right tool. Hint: it's
a "protein
specific analysis"
Mark
Thanks
2011/1/4 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>>
On 4/01/2011 8:33 PM, ahmet yıldırım wrote:
Hi,
How can I calculate the percentages (alpha
helix,
beta
sheet, coil ...) of secondary structure?
Look in manual section 7.4 for a suitable tool.
Mark
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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========================================
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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========================================
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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