VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Sat Jul 28 2007 - 15:02:54 CDT

Harish Vashisth kindly pointed out that there's a missing ] at the end of the statement as I reproduced it in my original message. However, entering the command correctly does still result in the behavior indicated below. Yes, I tried again & made double sure it was there.

Thanks!

Irene

----------------------------------------
> From: einew_at_hotmail.com
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: problem with rmsd-fullthrottle
> Date: Fri, 27 Jul 2007 10:16:54 -1000
>
>
> I load my psf file & my dcd file into vmd & open a Tk console. I type
> source residue_rmsd.tcl and follow it by
>
> set sel_resid [[atomselect top "protein and alpha"] get resid
>
> A set of numbers spits out.
>
> I then type
>
> source rmsd-fullthrottle.tcl
>
> I get a blue message saying "Calculating rmsd for frame 0..."
> Shortly thereafter a red message comes up "measure rmsd: no atoms selected".
>
> However, if I type echo $sel_resid, I get the list of numbers that was printed to the console from the sel_resid command.
>
> If I try to add sel_resid to the line calling rmsd-fullthrottle, w or w/out the leading $, I get a message about wrong arguments.
>
> If I do as recommended on http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node13.html & type
>
> rmsd_residue_over_time top $sel_resid
>
> I get the same blue & red messages.
>
> There are no new files containing data from any of these attempts. What should I do?
>
> Thanks!
> Irene Newhouse
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_________________________________________________________________
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