VMD-L Mailing List

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Tue Sep 25 2012 - 12:47:41 CDT

--- On Tue, 9/25/12, flavio seixas <oivalf_nix_at_yahoo.com> wrote:

> From: flavio seixas <oivalf_nix_at_yahoo.com>
> Subject: RE: vmd-l: Big DCD file help
> To: "BrianBennion" <Bennion1_at_llnl.gov>
> Date: Tuesday, September 25, 2012, 6:47 PM
> Hi Brian, thanks again for your
> help.
>
> But still does not work. The rmsd values appeasr listed at
> TKwindow not in a file.
>
> Any other suggestion?
>
> Here is the final script:
>
>
> proc myrmsd { frame } {
>    global ref sel all outfile
>    $all move [measure fit $sel $ref]
>    puts "$frame: [measure rmsd $sel $ref]"
> }
> set mol [mol addfile CALDHmT178_wb_min4.pdb type pdb waitfor
> all]
> set all [atomselect $mol all]
> set ref [atomselect $mol "name CA" frame 0]
> set sel [atomselect $mol "name CA"]
> set outfile [open rmsd.dat w]
> puts $outfile "[measure rmsd $sel $ref]"
> bigdcd myrmsd dcd CALDHmT178_wb_eq5.dcd
> bigdcd_wait
> close $outfile
>
>
> Regards,
>
> Flavio
>
>
>
>
> --- On Tue, 9/25/12, Bennion, Brian <Bennion1_at_llnl.gov>
> wrote:
>
> > From: Bennion, Brian <Bennion1_at_llnl.gov>
> > Subject: RE: vmd-l: Big DCD file help
> > To: "flavio seixas" <oivalf_nix_at_yahoo.com>
> > Date: Tuesday, September 25, 2012, 5:58 PM
> > You need set the filehandle to global
> > in the global section of myrmsd.
> >
> > Global ref sel all outfile
> >
> > -----Original Message-----
> > From: flavio seixas [mailto:oivalf_nix_at_yahoo.com]
> >
> > Sent: Tuesday, September 25, 2012 9:56 AM
> > To: VMD List; Bennion, Brian
> > Subject: RE: vmd-l: Big DCD file help
> >
> > Hi Brian, many thanks for your help.
> >
> > I modify the scipt to:
> >
> > proc myrmsd { frame } {
> >    global ref sel all
> >    $all move [measure fit $sel $ref]
> >    puts "$frame: [measure rmsd $sel $ref]"
> >  }
> > set mol [mol addfile CALDHmT178_wb_min4.coor type pdb
> > waitfor all] set all [atomselect $mol all] set ref
> > [atomselect $mol "name CA" frame 0] set sel [atomselect
> $mol
> > "name CA"] set outfile [open rmsd.dat w]; puts
> $outfile
> > "[measure rmsd $sel $ref]"
> > bigdcd myrmsd dcd CALDHmT178_wb_eq5.dcd
> > bigdcd_wait
> > close $outfile
> >
> >
> > But it still does not work.
> > Maybe is because I am not sure about how to "Make it
> > global"
> >
> > Sorry about the basic question, but I am not familiar
> with
> > tcl scripts. I google it, but no clues about what to
> do...
> >
> > Any advice?
> >
> > Regards,
> >
> > Flavio
> >
> >
> >
> > --- On Tue, 9/25/12, Bennion, Brian <Bennion1_at_llnl.gov>
> > wrote:
> >
> > > From: Bennion, Brian <Bennion1_at_llnl.gov>
> > > Subject: RE: vmd-l: Big DCD file help
> > > To: "flavio seixas" <oivalf_nix_at_yahoo.com>,
> > "VMD List"
> > > <vmd-l_at_ks.uiuc.edu>
> > > Date: Tuesday, September 25, 2012, 5:43 PM
> > >
> > > Not tested
> > >
> > > Open a file
> > > Set fh1 [open "rmsd.plt" w]
> > > Make it global and in the proc add
> > >
> > > puts $fh1 "$frame: [measure rmsd $sel $ref]"
> > >
> > > -----Original Message-----
> > > From: owner-vmd-l_at_ks.uiuc.edu
> > > [mailto:owner-vmd-l_at_ks.uiuc.edu]
> > > On Behalf Of flavio seixas
> > > Sent: Tuesday, September 25, 2012 8:16 AM
> > > To: VMD List
> > > Subject: vmd-l: Big DCD file help
> > >
> > > Hi,
> > >
> > > I am trying to calculate rmsd from my dcd files.
> The
> > namd rmsd tcl
> > > script is working fine. Unfortunately the values
> > appears listed in tk
> > > window and can not be copied at all.
> > > Is possible to put the rmsd values in a file?
> > >
> > > This is my script:
> > >
> > >
> > > proc myrmsd { frame } {
> > >    global ref sel all
> > >    $all move [measure fit $sel $ref]
> > >    puts "$frame: [measure rmsd $sel $ref]"
> > >  }
> > > set mol [mol addfile CALDHmT178_wb_min4.pdb type
> pdb
> > waitfor all] set
> > > all [atomselect $mol all] set ref [atomselect
> $mol
> > "name CA" frame 0]
> > > set sel [atomselect $mol "name CA"] bigdcd myrmsd
> dcd
> > > CALDHmT178_wb_eq5.dcd bigdcd_wait
> > >
> > >
> > >
> >
>