VMD-L Mailing List

From: Falgun Shah (fhshah_at_olemiss.edu)
Date: Fri Mar 13 2009 - 08:56:31 CDT

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