From: ban arn (ban.arn_at_gmail.com)
Date: Wed Jul 28 2010 - 08:01:54 CDT

Dear Leo

Thanks.

Balaji

On Wed, Jul 28, 2010 at 1:59 PM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>wrote:

> OK, so I did answer your question already:
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/16203.html
>
> Leo
>
> On Wed, Jul 28, 2010 at 2:55 PM, ban arn <ban.arn_at_gmail.com> wrote:
> > Dear Leo
> >
> > Thanks.
> >
> > This is the command i'm using
> >
> > "rmsd_matrix -mol top -seltext name CA -frames all -fit none -o
> 2d_plot.txt"
> > usage: rmsd_matrix ?-arg var?...
> > -mol <molid> (default: top)
> > -seltext <selection text> (default: backbone)
> > -frames <begin:end> or <begin:step:end> or all or now (default: all)
> > -fit <selection text> (default: backbone)
> > -o <filename>
> > error: empty argument list or odd number of arguments -mol top -seltext
> name
> > CA -frames all -fit none -o 2d_plot.txt
> >
> > Many Thanks
> > Balaji
> >
> > On Wed, Jul 28, 2010 at 1:50 PM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>
> > wrote:
> >>
> >> On Wed, Jul 28, 2010 at 2:45 PM, ban arn <ban.arn_at_gmail.com> wrote:
> >> > Dear Leonard
> >> >
> >> > Thanks for the reply.
> >> >
> >> > I have saved trajectories containing only CA atoms.
> >> >
> >> > And in the command, i'm mentioning c-alpha atoms as "name CA in
> >> > seltext",
> >> > but it shows error as atomselect: cannot parse selection text: CA.
> >> >
> >> > Could you please tell me how to specify c-alpha atoms so that VMD can
> >> > read
> >> > it.
> >>
> >> Didn't I answer your question yesterday? What exactly is the command
> >> that you are using (please copy and paste it)?
> >>
> >> Leo
> >>
> >> > Many Thanks
> >> > Balaji
> >> >
> >> > On Wed, Jul 28, 2010 at 12:24 PM, Leonardo Trabuco
> >> > <ltrabuco_at_ks.uiuc.edu>
> >> > wrote:
> >> >>
> >> >> Dear Balaji,
> >> >>
> >> >> On Wed, Jul 28, 2010 at 12:50 PM, ban arn <ban.arn_at_gmail.com> wrote:
> >> >> > Dear All
> >> >> >
> >> >> > I would like to plot 2D rmsd matrix for C-alpha atoms through my
> >> >> > trajectories.
> >> >> >
> >> >> > Is any script available for this in VMD
> >> >>
> >> >>
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/rmsd_matrix/
> >> >>
> >> >> Cheers,
> >> >> Leo
> >> >>
> >> >> > Kindly advice.
> >> >> >
> >> >> > Many Thanks
> >> >> > Balaji
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Leonardo Trabuco, Ph.D.
> >> >> CellNetworks, BioQuant
> >> >> University of Heidelberg, Germany
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Leonardo Trabuco, Ph.D.
> >> CellNetworks, BioQuant
> >> University of Heidelberg, Germany
> >
> >
>
>
>
> --
> Leonardo Trabuco, Ph.D.
> CellNetworks, BioQuant
> University of Heidelberg, Germany
>