VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 11 2003 - 17:24:22 CDT

Mike,
  I found a few errors in the script you sent me, but I do see
some strange behavior with the wait calls as it executes. Let me
take a look at it and get back to you after I do some more tests.
In my tests, it behaves exactly the same on both Windows and Unix,
so that much I've determined so far. The last wait call seems to
work fine, but the ones in the middle don't actually pause execution
as far as I can tell. There are some tricky things at issue with
the implementation of 'wait' commands. For now, try using this
"mywait" command I just wrote for you in Tcl:

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

I've attached the new version of the script to this email.
Let me know if you have trouble using it.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 11, 2003 at 04:54:58PM -0500, Michael Redmond wrote:
> Here is the script and the pdb file. For the script to work, I guess the
> pdb file needs to be in the root directory. I could not use relative
> location of the script directory of the set directory to find the pdb file.
> Is there a way to do that as well? Or is full, absolute path always
> required in the "play" file?
> Thanks
> Mike
> ---
> At 04:47 PM 4/11/2003 -0500, you wrote:
>
> >Dear Michael,
> > Can you send me a copy of your script? The 'wait' command works
> >for me in Windows on VMD 1.8.1b1, so unless I fixed some code and
> >then forgot about it since December, I'm not sure why you'd see
> >different behavior between Unix and Windows versions. If you want
> >to try testing VMD 1.8.1b1 and see if it behaves at all differently,
> >I can give you a copy of the new code. In any case, if you send me a copy
> >of your script, that'd also be helpful.
> >
> >Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Fri, Apr 11, 2003 at 04:28:43PM -0500, Michael Redmond wrote:
> >> John,
> >> I am using vmd -e dna_vmd where the dna_vmd contains the commands:
> >>
> >> wait 15000 (just to see if it made a difference)
> >> and more typically
> >> wait 5
> >>
> >> But these have no effect. I am not sure I know how to control "source" vs
> >> "play" functionality. I will add the .vmd extension to my command file,
> >but
> >> I doubt that is what makes the difference.
> >>
> >> One thing is that I built this script using the original .vmdrc because
> >> that was the only way to use scripts in older Windows versions. I don't
> >> think I still need all the overhead of the .vmdrc script anymore, and
> >maybe
> >> that is causing the problems.?
> >>
> >> Thanks
> >> Mike
> >> ---
> >> At 03:52 PM 4/11/2003 -0500, John Stone wrote:
> >>
> >> >Mike,
> >> > I do remember talking about this before, but as far as I recall
> >> >the specific problem you're having isn't so much wait but the way
> >> >wait behaves inside of Tcl procs etc. If you use wait in a script
> >> >that you "play" it should work fine. If you use wait in a script
> >> >that you "source" it may or may not work. Let me know if you need
> >> >more help with this. Running "vmd -e script.vmd" is equivalent to doing
> >> >"play script.vmd" inside of the VMD console. If you're using source
> >> >rather than play, this would likely explain your problem.
> >> >Let me know if you need more help with this or if my suggestion
> >> >doesn't cure your problem.
> >> >
> >> >Thanks,
> >> > John Stone
> >> > vmd_at_ks.uiuc.edu
> >> >
> >> >On Fri, Apr 11, 2003 at 03:43:13PM -0500, Michael Redmond wrote:
> >> >> I think we went through this once before, but I can't find it in the
> >> >list.
> >> >> I have a VMD script with wait commands in it that works under Unix.
> >Under
> >> >> Windows 2000, there are no waits, it just plows right through to the
> >end.
> >> >>
> >> >> I am now running 1.8 and at now scripts work (-e option), but not wait
> >> >> commands.
> >> >>
> >> >> Thanks
> >> >> Mike Redmond
> >> >>
> >> >
> >> >--
> >> >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
> >>
> >
> >--
> >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 

-- 
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