Anitha wrote:
my header starts as
# g_sas is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@ title "Area per residue"
@ xaxis label "Residue"
@ yaxis label "Area (nm\S2\N)"
@TYPE xy
1 0.846565 0.312334
2 0.598 0.189911
3 0.837035 0.363443
4 1.14936 0.304359
5 0.630063 0.233607
6 0.625571 0.321569
7 0.261401 0.240533
8 0.0940011 0.0872611
i`m not able to understand what the second and third column represents....
This is a plot of surface area per residue, and as the y-axis label indicates,
you have area in square nm. The second column is the area, the third column is
the fluctuation. The last column is not immediately obvious, but from the code
it is clear (and an identical question posted to this list not too long ago).
-Justin
On Fri, Jul 30, 2010 at 4:33 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Anitha wrote:
In the headers file also i didn`t get the answer about those
lines....
Well, what do they say?
-Justin
On Fri, Jul 30, 2010 at 4:01 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Anitha wrote:
I executed the following command.
g_sas -s topol.tpr -f traj.xtc -or resarea.xvg -o area.xvg
xmgrace -nxy resarea.xvg
I have chosen the protein group for surface calculation
and output.
I get two sets of values: one is bigger (black) than the
other
(red).
I have checked the manual and other sources, but I could
not find an
answer about the black and red line. What does red and black
line shows?
Read the headers of the .xvg file.
-Justin
-- S.Anitha
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
S.Anitha
--
========================================
Justin A. Lemkul
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
S.Anitha
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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