VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Nov 04 2001 - 11:02:59 CST

Dear Tom,
  The animatepdbs script is subject to the same limitations
that normal trajectories are, since it results in the sequence
of PDB files being read in as new "frames" of a trajectory.
You could modify it however, to create a new script that would
load in one PDB at a time, color it the way you want, draw it
(or render with snapshot etc) and then delete it, repeating until
all frames are done.

In order to run scripts in VMD, you need to "source" them, otherwise
they get interpreted as a shell command as happened to you below. The
correct way to run a script in VMD is to source the script file first,
like this:

vmd > source animatepdbs.txt
vmd > animatepdbs 0 2 "%d.pdb"

Let us know if you need more help on this.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Nov 04, 2001 at 10:02:35AM -0500, tom keyes wrote:
> The animatepdbs script looks to me like it should allow frame-dependent
> coloring, so long as I write a zillion little files instead of one big one.
> However below is what my first attempt gave. I know nothing of Tcl, this is
> Mac OS X. I opened VMD, made my 'graphics' choices, and attempted to run
> the script from console. Is there something else I need to do? TIA for any
> suggestions....Tom
>
> vmd > animatepdbs 0 2 "%d.pdb"
> ./animatepdbs: command not found: proc [26]
> ./animatepdbs: command not found: incr [28]
> ./animatepdbs: command not found: puts [29]
> ./animatepdbs: command not found: mol [30]
> ./animatepdbs: command not found: puts [32]
> ./animatepdbs: parse error near `{set' [33]
> ./animatepdbs: command not found: animate [35]
> ./animatepdbs: parse error near `}' [36]
> ./animatepdbs: parse error near `}' [37]
> child process exited abnormally
> vmd >
> 

-- 
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