VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Mar 11 2009 - 11:30:30 CDT

On Wed, 2009-03-11 at 10:36 -0500, John Stone 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.

john is correct, there is an updated and improved version of
the script, and its been around for a bit, yet not in bochum,
but in the VMD biocore biofs at:
https://biocore-s.ks.uiuc.edu/biocore/biofs/VMD%
20(Public)/src/rpm/vmd_draw_lib.tcl

the tutorial in bochum is still online because people are asking me to
keep it. it is however practically abandoned, i left bochum almost four
years ago, don't support CPMD anymore, and am currently working on more
low-level programming issues (in part also in VMD). it is in dire need
of an update and caring hands to keep it a useful resource for learning
advanced scripting in VMD. there have been a few volunteers that showed
interest so far to update it and make it even more general, but none
came through until now.

cheers,
   axel.
>
> 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>
> > >
> > > 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 

-- 
=======================================================================
Dr. Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
Associate Director - Center for Molecular Modeling - U. of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
  tel: 1-215-898-1582,   fax: 1-215-573-6233,   cell: 1-215-520-7732
=======================================================================