VMD-L Mailing List

From: Falgun Shah (fhshah_at_olemiss.edu)
Date: Fri Mar 13 2009 - 10:40:47 CDT

Thanks john! that worked!

On Fri, Mar 13, 2009 at 10:14 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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
> >
> > > <
> > >
> 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/><
> > > 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/ <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