VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 13 2009 - 10:14:21 CDT

Yes, you can change the active color with "draw color" or
"graphics $mol color" etc, as described in the VMD User's Guide.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 13, 2009 at 08:56:31AM -0500, Falgun Shah wrote:
> Dear John and axel
>
> Thanks very much for providing the updated script. that worked for me. I
> have one more question. is it possible to change the color of object such as
> vector or arrow or spring. please let me know.
>
> On Wed, Mar 11, 2009 at 10:36 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Hi,
> > I'd ask Axel about this bug since it's his script. The one in the VMD
> > User's Guide works fine, but doesn't provide the flexibility that Axel's
> > is attempting to, that said, the version of Axel's script you're using
> > below does have some odd behavior.
> >
> > For now, just use this script (from the VMD User's Guide) instead:
> >
> > proc vmd_draw_arrow {mol start end} {
> > # an arrow is made of a cylinder and a cone
> > set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
> > graphics $mol cylinder $start $middle radius 0.15
> > graphics $mol cone $middle $end radius 0.25
> > }
> >
> > You'll want to check with Axel to see if he has a newer version of his
> > script that addresses the problem you found.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Mon, Mar 09, 2009 at 05:55:58PM -0500, Falgun Shah wrote:
> > > 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>
> > <
> > http://www.theochem.ruhr-uni-bochum.de/%7Eaxel.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
> >
> > --
> > 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 

-- 
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/      Fax: 217-244-6078