[gmx-users] converting .xpm to .eps

[bipin singh]

Have you tried the first suggestion too ??

If even that does not worked then something wrong with your system.


On Fri, Dec 20, 2013 at 5:06 PM, Nidhi Jatana <nidhijatana at bic-svc.ac.in>wrote:

> I tried increasing the grid spacing by setting -bin from default of 0.02 to
> 0.04 and decreased it as well to 0.01. Butives the same of no help. It
> still gives the same error.
>
>
> On Fri, Dec 20, 2013 at 4:19 PM, bipin singh <bipinelmat at gmail.com> wrote:
>
> > You may try to produce the xpm matrix for small portion of your
> trajectory
> > (using -b and -e option) and then try xpm2ps on it to check whether it
> > works for small size xpm matrix or not.
> >
> >  OR you can increase the grid spacing with -bin option of g_densmap while
> > generating the xpm matrix for the whole trajectory.
> >
> >
> > On Fri, Dec 20, 2013 at 3:55 PM, Nidhi Jatana <nidhijatana at bic-svc.ac.in
> > >wrote:
> >
> > > How do you fix the matrix size? Should I do it while generation of .xpm
> > > file or while converting it to .eps and using which option?
> > >
> > > Regards
> > > Nidhi
> > >
> > >
> > > On Fri, Dec 20, 2013 at 3:35 PM, Carsten Kutzner <ckutzne at gwdg.de>
> > wrote:
> > >
> > > > On 12/20/2013 10:09 AM, bipin singh wrote:
> > > >
> > > >> Not sure, might be something going wrong due to large dimension of
> > your
> > > >> matrix. Which Gromacs version you are using. Others may provide some
> > > >> clues.
> > > >>
> > > > I just tried with a 483 x 486 matrix which went smoothly.
> > > > You could try to narrow down the problem.
> > > > See whether it works with other input data for example.
> > > > Check whether it works on another machine.
> > > >
> > > > Carsten
> > > >
> > > >
> > > >>
> > > >> On Fri, Dec 20, 2013 at 10:04 AM, Nidhi Jatana <
> > > nidhijatana at bic-svc.ac.in
> > > >> >wrote:
> > > >>
> > > >>  Dear Sir/Madam
> > > >>> Please find attached the file containing the error.
> > > >>>
> > > >>> Thanking you
> > > >>>
> > > >>> Regards
> > > >>> --
> > > >>> Nidhi Jatana
> > > >>> Senior Research Fellow
> > > >>> Bioinformatics Center
> > > >>> Sri Venkateswara College
> > > >>> (University of Delhi)
> > > >>> Dhaula Kuan
> > > >>> New Delhi-110021.
> > > >>>
> > > >>>
> > > >>>
> > > >>> On Thu, Dec 19, 2013 at 7:44 PM, Carsten Kutzner <ckutzne at gwdg.de>
> > > >>> wrote:
> > > >>>
> > > >>>  On 12/19/2013 12:53 PM, Nidhi Jatana wrote:
> > > >>>>
> > > >>>>  Dear Sir/Madam
> > > >>>>> I generated the atomic density plot using g_densmap by giving the
> > > >>>>> following
> > > >>>>> command:
> > > >>>>> g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm
> > > >>>>>
> > > >>>>> The calculation completed successfully but when I am trying to
> > > convert
> > > >>>>> .xpm
> > > >>>>> file to .eps file using xpm2ps command, its giving error and
> > aborts.
> > > >>>>>
> > > >>>>>  What is the error message?
> > > >>>>
> > > >>>> If I use your set of commands with Gromacs 4.6.4, I can
> successfully
> > > >>>>
> > > >>> create
> > > >>>
> > > >>>> an EPS file.
> > > >>>>
> > > >>>> Carsten
> > > >>>>
> > > >>>>
> > > >>>>  xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm
> > > >>>>>
> > > >>>>> I have tried many options with setting -bx and -by but of no
> help.
> > I
> > > >>>>>
> > > >>>> also
> > > >>>
> > > >>>> tried taking the .m2p file but the problem persist. Please find
> > > attached
> > > >>>>> the .m2p file for reference. Please help me with this.
> > > >>>>>
> > > >>>>> Thanking you
> > > >>>>>
> > > >>>>> Regards
> > > >>>>>    --
> > > >>>>> Nidhi Jatana
> > > >>>>> Senior Research Fellow
> > > >>>>> Bioinformatics Center
> > > >>>>> Sri Venkateswara College
> > > >>>>> (University of Delhi)
> > > >>>>> Dhaula Kuan
> > > >>>>> New Delhi-110021.
> > > >>>>>
> > > >>>>>
> > > >>>>>
> > > >>>>>  --
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> > >
> > > --
> > > Nidhi Jatana
> > > Senior Research Fellow
> > > Bioinformatics Center
> > > Sri Venkateswara College
> > > (University of Delhi)
> > > Dhaula Kuan
> > > New Delhi-110021.
> > > --
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> > --
> >
> >
> >
> > *--------------------Thanks and Regards,Bipin Singh*
> > --
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>
>
> --
> Nidhi Jatana
> Senior Research Fellow
> Bioinformatics Center
> Sri Venkateswara College
> (University of Delhi)
> Dhaula Kuan
> New Delhi-110021.
> --
> Gromacs Users mailing list
>
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-- 



*--------------------Thanks and Regards,Bipin Singh*