VMD-L Mailing List

From: Parminder Mankoo (pmankoo1_at_jhu.edu)
Date: Sat Jun 30 2007 - 22:06:43 CDT

Thank you so much Leo!

Your modification works very well.

Best,
Parminder

On Jun 30, 2007, at 9:14 PM, Leonardo Trabuco wrote:

> Hi Parminder,
>
> On Sat, Jun 30, 2007 at 08:09:18PM -0400, Parminder Mankoo wrote:
>> I am trying to write "RMSF" from 1500ps trajectory for 900 residues.
>> I use following 4 line script to do it. However, the output is not
>> what I expected. I want to get RMSF of each residue to print on a
>> separate line so I could plot it easily. Does anyone has a working
>> script of rmsf for to try or suggest any changes to following script?
>>
>> thanks, parminder
>>
>> set outfile [open rmsf.dat w]
>> set sel [atomselect top "name CA"]
>> puts $outfile "[measure rmsf $sel first 1 last 1500 step 1]"
>> close $outfile
>
> This should do the trick:
>
> for {set i 0} {$i < [$sel num]} {incr i} {
> puts $outfile "[expr {$i+1}] [lindex $rmsf $i]"
> }
>
> Cheers,
> Leo
>
> --
> Leonardo Trabuco, Ph.D. student
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign