VMD-L Mailing List

From: Falgun Shah (fhshah_at_olemiss.edu)
Date: Mon Mar 09 2009 - 17:55:58 CDT

Dear John

Thanks very much for your suggestion. I used arrow.tcl to plot the direction
using two coordinates
i am able to execute the command [draw arrow {15.162 -29.097 9.795} {11.492
-9.597 4.865}] after sourcing vmd_draw_arrow.tcl script. However, instead of
arrow it is drawing only cylinder and (not plotting the cone part of arrow).
Do i need to modify the script or i am doing mistake in executing commmand.

The script vmd_draw_arrow.tcl is pasted here. Thanks
vmd extension procedures
#
# $Id: vmd_draw_arrow.tcl,v 1.1 2005/01/03 14:06:39 akohlmey Exp $

# this is an improved version of the 'draw arrow' extension
# as described in the user's guide. this version also returns
# the list of graphic ids for easy selective deletion.
proc vmd_draw_arrow {mol start end {scale 1.0} {res 10} {radius 0.2}} {
  set middle [vecadd $start [vecscale $scale [vecsub $end $start]]]
  return [list \
      [graphics $mol cylinder $start $middle radius $radius \
                resolution $res filled yes] \
      [graphics $mol cone $middle $end radius [expr $radius * 0.6] \
                resolution $res ] \
  ]
}

# draw a whole list of arrows. a convenience functions to draw a
# lot of vectors easily.
# field has to be a list of pairs of xyz triples (start- and endpoint).
# the function returns a list of the graphics ids for easy deletion.
proc vmd_draw_arrowfield {mol field {scale 1.0} {res 10} {radius 0.2}} {
    set gids ""
    foreach i $field {
        lassign $i cnt vec
        append gids " " [vmd_draw_arrow $mol $cnt $vec $scale $res $radius]
    }
    return $gids
}

############################################################
# Local Variables:
# mode: tcl
# time-stamp-format: "%u %02d.%02m.%y %02H:%02M:%02S %s"
# End:
############################################################

On Tue, Mar 3, 2009 at 3:51 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> I'd suggest using MSMS for your surface representation, as it gives
> nice looking surfaces. You can draw springs and other graphical objects
> using the "draw" or "graphics" commands in VMD. There are various example
> scripts for drawing arrows etc in the VMD/CPMD tutorial here:
>
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect1>
>
> There's an old spring drawing script here:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/spring/
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Mar 01, 2009 at 03:23:12PM -0600, Falgun Shah wrote:
> > Dear Vmd users
> >
> > I am doing constant velocity smd simulation of the protein of my
> interest. I
> > want to generate final image of the protein in surface representation
> along
> > with virtual spring showing 3 direction of egress for my ligand. Please
> let
> > me know the best way to generate molecular surface of protein binding
> site
> > and how to insert spring between COM of the smd atoms and the calculated
> > direction. Your recommendations are most welcome. Thanks in advance.
> > --
> > Falgun H shah
> > PhD candidate (3rd year)
> > Department of Medicinal Chemistry
> > 2028, Natural Product Center
> > University of Mississippi
> >
> > Ph No: 6629151286(O)
> > 662 801 5667(M)
> > email: fhshah_at_olemiss.edu
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi
Ph No: 6629151286(O)
          662 801 5667(M)
email: fhshah_at_olemiss.edu