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From: Irene Newhouse (einew_at_hotmail.com)
Date: Fri Jul 27 2007 - 15:16:54 CDT

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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