VMD-L Mailing List

From: Fahimeh Baftizadeh (fahimeh.baftizadeh_at_googlemail.com)
Date: Fri Jan 14 2011 - 12:26:40 CST

Thank you very much Alex,
Finally ;-) with a littel bit of coding I managed to generate the correct
format for "cube" file and then read them sequentially with your script with
very small modification that I did.
Now I like to add some representaion, like VolumeSlice, and look at it
during the trajectory, but I think there is something worng going on , It
update the isosurface representation correctly but not the VolumeSlice
representation!
Can you help me to find out the problem ?! I am sorry but I am very new in
tcl programming :-(
He

# $Id: au-iso.vmd,v 1.2 2004/05/21 15:50:29 akohlmey Exp $
# Display settings
display projection Orthographic
display nearclip set 0.000000
display farclip set 10.000000
display depthcue off
# store the molecule id for later use
set step 188
set start 11
set updmol [mol new {out_10.cube} type cube waitfor all]
for { set i $start} {$i < $step } { incr i } {
mol addfile out_${i}.cube type cube waitfor all
}

mol delrep 0 top
mol representation Isosurface 0.04 0.0 0.0 0.0
mol color ColorID 15
mol selection {all}
mol addrep top
mol representation VolumeSlice
#mol color ColorID 5
mol selection {all}

# store name of the isosurface representation (id=3) for later use
mol addrep top
set updrep [mol repname top 0]
set updrep [mol repname top 1]
#mol rename top {Golden Shot}

rotate z by -90
rotate x by -90
rotate x by 2
rotate y by 3
rotate x by 2

# use the volumetric data set for the isosurface corresponding to the frame.
# $updmol contains the id of the molecule and $updrep the (unique) name of
# the isosurface representation
#
proc update_iso {args} {
    global updmol
    global updrep

    # get representation id and return if invalid
    set repid [mol repindex $updmol $updrep]
    if {$repid < 0} { return }

    # update representation but replace the data set
    # id with the current frame number.
    set frame [molinfo $updmol get frame]
    lassign [molinfo $updmol get "{rep $repid}"] rep
    mol representation [lreplace $rep 2 2 $frame]
    mol modrep $repid $updmol
}

trace variable vmd_frame($updmol) w update_iso
animate goto 0

On Tue, Jan 11, 2011 at 12:29 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Mon, Jan 10, 2011 at 4:29 PM, Fahimeh Baftizadeh
> <fahimeh.baftizadeh_at_googlemail.com> wrote:
>
> fahimeh,
>
> > thanks John for your reply.
> > Let me make my question more clear.
> > I have a grid of point which they have intensity as a function of time,
> they
> > are fixed in the space, What I would like to see is
> > 1- their intensity change with time (like changing the colors).
> > 2- then I would like to apply also the volume slice to have more visual
> > information.
>
> what you describe is a visualization problem, that is usually
> handled by tools like ParaView (http://paraview.org)
> or OpenDX (http://www.opendx.org), and others most of which
> are commercial applications. they allow you much more flexible
> reading and processing of data compared to VMD.
>
> > I was thinking of generating a file.dx ... but maybe i need a little bit
> of
> > tcl scripting in order to generate a movie, not a single frame.
>
> yes. you can load multiple volumetric data sets and then show
> only one of them. here is an old script of mine that does this
>
> http://klein-group.icms.temple.edu/cpmd-vmd/files/au-iso.vmd
>
> with "cube" files (which are grids that also include atoms) you
> can use this with .dx files just as well. the multi-molanim GUI
> that john mentioned more-or-less does the same thing, but with
> whole "molecules" (which in VMD-speak can also refer to a
> single graphics visualization without any atoms).
>
>
> cheers,
> axel.
>
>
>
>
> > Thanks in advance
> > Fahimeh
> >
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
> 

-- 
--------------------------------------------------------------------------------------------------------------
Fahimeh Baftizadeh
SISSA, via Bonomea, 265
34136 Trieste, ITALY
email : fbafti_at_sissa.it
           fahimeh.baftizadeh_at_gmail.com
phone : +39-040-3787-302