From: Alison Grinthal (
Date: Fri Jul 10 2009 - 08:31:26 CDT

I'm trying to measure the rmsf for each of the alpha carbons in a protein,
using the following script:

set fp [open "rmsf.dat" w]
set sel [atomselect top "resid 1 to 288 and name CA"]
for {set i 0} {$i < [$sel num]} {incr i} {
     set rmsf [measure rmsf $sel first 1 last 3991 step 10]
     puts $fp "[expr {$i+1}] [lindex $rmsf $i]"
close $fp

It seems to work fine (no error messages, and I get a plottable list of
values), except that instead of getting a list with all 288
CA's, I get 223. I tried with a series of trajectories and the same thing
happens with each of them, so I'm wondering if it might be something
wrong with the script. The psf and dcd files seem fine - VMD recognizes
all alpha carbons for purposes of display, and I don't get any messages
about irregular bonds when reading in the files. I'd be grateful for any
advice on what I could be doing wrong or what else I can do to figure it
out. Thanks a lot.