[gmx-users] query about .xpm file

[sangeeta kundu]

Dear Sir,
     While viewing the trajectory of a 10ns MD
simulation run , .xpm file is generated that can be
converted into an .eps file , but the problem I am
facing is in the time scale (X axis) in spite of
exhibiting the scale it is giving a black bar, I used
diifeerent permutation combination of -bx and -by ,
the Secondary str file  improves, but no improvement
in the time scale, rather  each time a black bar is
displayed.
How can I get the appropriate time scale?
regards
SANGEETA
--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> sangeeta kundu wrote:
> > Dear Sir,
> > 
> >     I converted  the output of do_dssp program
> (.xpm
> > file) into an .eps file by the command xpm2ps,I
> also
> > specified the size by -size command, but the
> problem
> > is that when I am observing the trajectory for
> > 10-200ps the output looks fine , but as I increase
> the
> > time scale from 100ps to 1/2 - 8/10 ns  I am
> observing
> > only a line, I mean to say as I increase the X
> axis,
> > the Y axis is being quenched, so it is not anyway
> > producing the correct data type,I can not
> understand
> > how to get rid of this problem , How can I
> visualise
> > the .xpm file, How can I convert it successfully
> into
> > a postscript file, so that every residue and the
> time
> > scale will be clearly visible, PLease help.
> > 
> specify an m2p input file where you set the y-size
> larger. alternatively 
> use -skip in do_dssp to get fewer point on the x
> axis.
> -- 
> David.
>
________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://folding.bmc.uu.se
>
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