VMD-L Mailing List

From: rainy908_at_yahoo.com
Date: Wed Dec 02 2009 - 20:22:50 CST

Hi John,

Thanks for getting back to me on this. Your suggestion worked. Now only to
make things more complicated :), what if I want to specify a transparent,
cylindrical-shaped bond between two beads, as well as an opaque,
cylindrical-shaped bond between another set of beads? I tried setting up my
tcl script as:

 set pos1 { 0 0 0 }
 set pos2 { 1 1 1 }
 set pos3 { 2 2 2 }
 set pos4 { 3 3 3 }

 draw material Transparent
 draw color silver
 draw cylinder $pos1 $pos2 radius 0.3

 draw material Opaque
 draw color black
 draw cylinder $pos2 $pos3 radius 0.3

However, when I reset the material to Opaque, the display shows that both
bonds are opaque. How should I write my script so that both transparent and
opaque materials are simultaneously shown? I presume I would have to make a
new representation?

Your resident newbie,
Lili

2009/12/2 John Stone <johns_at_ks.uiuc.edu>

>
> Hi,
> Most likely the contents of $pos1 and $pos2 are incorrectly formatted,
> and you didn't set the material properly:
>
> Try this:
> set pos1 { 0 0 0 }
> set pos2 { 1 1 1 }
> draw material Transparent
> draw color silver
> draw cylinder $pos1 $pos2 radius 0.3
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Dec 02, 2009 at 03:29:24PM -0800, rainy908_at_yahoo.com wrote:
> > Hi,
> >
> > I apologize if this question has been asked previously, but I am
> curious
> > to know if there is a way to draw a silver-colored cylinder in VMD?
> My
> > TCL script so far includes:
> >
> > material Transparent
> > draw color silver
> > draw cylinder $pos1 $pos2 radius 0.3
> >
> > However, my commands only result in an error with no cylinder
> > (representing a bond between 2 beads) drawn.
> > If anybody has any knowledge on this issue, I would be most
> appreciative
> > of your help.
> >
> > Thank you,
> > rainy908
>
> --
> 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
>