[gmx-users] About .xvg file display

[Marc Vogt]

This data file has a string as the third entry.  
when using nxy, it is like having

x y1 y2 y3 y4 etc...
x y1 y2 y3 y4 etc...
x y1 y2 y3 y4 etc...
x y1 y2 y3 y4 etc...

your data looks like

-121.702  110.685  ALA-2
-83.2156  127.886  ALA-2
-104.815  141.868  ALA-2
-113.169  145.209  ALA-2

so it is trying to make a plot using -121.702 for x and 110.685 as y
for one set
and  -121.702 for x with ALA-2 for y as another set. As you can imagine,
it is having a hard time figuring out at what point to place ALA-2
on an axis that has units of degrees.

This looks like a Ramachandran Plot from the file.  You don't want to
do nxy for this.  It should look fine without it.
You would use nxy for something like the output of do_dssp.  Each different
y will be for total secondary structure, beta, alpha etc.  

I don't understand your original post though.  Grace recognizes xvg.
I don't know what .arg is.  It is easy to convert from any format.
Grace only needs

x y
x y
x y

the other lines are comments and formatting.  


hope this helps,

Marc


> 
> Thank you for your reply. But there're a error as below:
> 
> Can not yet use strings when reading in data as NXY
> 
> 
> My .xvg file is such:
> 
> # This file was created by
> /home/zeng/chgy/para-gromacs/x86_64-unknown-linux-gnu/bin/g_rama
> # which is part of G R O M A C S:
> # Gravel Rubs Often Many Awfully Cauterized Sores
> # All this happened at: Thu Feb 24 09:57:13 2005
> #
> @    title "Ramachandran Plot"
> @    xaxis  label "Phi"
> @    yaxis  label "Psi"
> @TYPE xy
> @    with g0
> @    s0 linestyle 0
> @    s0 color 1
> @ view 0.2, 0.2, 0.8, 0.8
> @ world xmin -180
> @ world ymin -180
> @ world xmax 180
> @ world ymax 180
> @    xaxis  tick on
> @    xaxis  tick major 60
> @    xaxis  tick minor 30
> @    yaxis  tick on
> @    yaxis  tick major 60
> @    yaxis  tick minor 30
> @ s0 symbol 2
> @ s0 symbol size 0.4
> @ s0 symbol fill 1
> -121.702  110.685  ALA-2
> -83.2156  127.886  ALA-2
> -104.815  141.868  ALA-2
> -113.169  145.209  ALA-2
> -108.397  135.535  ALA-2
> -119.456  152.434  ALA-2
> -115.213  126.655  ALA-2
> -121.497  129.253  ALA-2
> -123.188  120.973  ALA-2
> -92.4551  148.262  ALA-2
> -107.355  144.254  ALA-2
> -108.533  155.093  ALA-2
> -94.4123  147.899  ALA-2
> -117.801  119.387  ALA-2
> -116.653  108.392  ALA-2
> -120.609  143.353  ALA-2
> -112.099  141.949  ALA-2
> ......
> 
> 
> Do you know what's wrong?
> 
> Yi
> 
> 
> On Thu, 24 Feb 2005, Andrey V. Golovin wrote:
> 
> > hi
> >
> > xmgrace -nxy whatever.xvg
> >
> >
> > ----
> > Best regards, Andrey
> > ----------------------------------------------------------------
> > Andrey V. Golovin
> > Ph.D,Professor assistant    tel: +7 (095) 939-5305
> > Bioengineering and
> > Bioinformatics Department
> > Moscow State University     fax: +7 (095) 939-3181
> > 119899 Moscow            E-mail: golovin at genebee.msu.su
> > Russia                      web: http://rnp-group.genebee.msu.su
> > -----------------------------------------------------------------
> >
> >
> > ---------- Original Message -----------
> > From: ygao at phase1.unl.edu
> > To: gmx-users at gromacs.org
> > Sent: Thu, 24 Feb 2005 11:45:20 -0600
> > Subject: [gmx-users] About .xvg file display
> >
> > > Hi,
> > >
> > > I'd like to use Grace to show a .xvg graph, but Grace only recognize
> > > the .arg format, how can I transfer .xvg into .arg? Thanks!
> > >
> > > Yi
> > >
> > > __________________________________________________________
> > >
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> __________________________________________________________
> 
> Department of Chemistry
> University of Nebraska -- Lincoln
> Lincoln, NE, USA 68508
> 
> Phone: 1-402-472-9982 (O)
>        1-402-310-4155 (M)
> Email: ygao at phase1.unl.edu
> 
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