VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 23 2004 - 13:18:57 CST

Jeff,
  Thanks for the note about the incorrect logging of 'mol new' on empty
molecules, I'll have to fix that. Regarding the "wait" command, 'wait' only
causes a delay when it is read on the console or from a "play" command which
executes Tcl scripts one line at a time. If you "source" the script, then
VMD loads the entire script all at once, and so the 'wait' command has
no effect. Does that make sense? Depending on what you want VMD to do
while it idles, you can write a little delay loop that does something
similar to wait like this:

proc mywait { waittime } {
  set starttime [clock seconds]
  while {[expr [clock seconds] - $starttime < $waittime]} {
  }
}

Let us know if you need more help with these items.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 19, 2004 at 07:40:59AM -0500, Hoch,Jeffrey wrote:
> Colleagues:
>
> I created a "blank" molecule and fixed it, to serve as a canvas for drawing fixed labels.
> However when I try to script the process I encounter errors creating the blank molecule.
> Curiously, when I "log" the process, the "mol new" command gets translated to "mol rename",
> and the log file doesn't "play" properly:
>
> # VMD for MACOSX, version 1.8.2 (December 4, 2003)
> # Log file 'junk.log', created by user jeffhoch
> menu files off
> menu files on
> animate style Loop
> display resetview
> mol new {/Users/jeffhoch/mosart/ls3-1.pdb} type {pdb} first 0 last -1 step 1 waitfor 1
> animate style Loop
> menu files off
> menu graphics off
> menu graphics on
> mol modstyle 0 0 Cartoon 2.100000 12.000000 5.000000
> menu graphics off
> animate style Loop
> mol rename 1 {molecule1}
> mol fix 1
> # VMD for MACOSX, version 1.8.2 (December 4, 2003)
> # end of log file.
>
> I've also encountered difficulty scripting the "wait" command: it works fine when entered
> into the terminal window interactively, but gets ignored when included in a script.
>
> As is obvious from the log file, I am using version 1.8.2 on Mac OSX (10.2.8).
>
> Suggestions?
>
>
> Yours,
>
> Jeff Hoch
> University of Connecticut Health Center
>
> 

-- 
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