VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 10 2009 - 10:42:33 CDT

Hi,
  What do you get if you do this:
set sel [atomselect top "resid 1 to 288 and name CA"]
$sel num

Do you get 288, or 223?

If you get 223, then you need to change your atom selection
so you're getting all of the CAs you intended to. Depending
on the numbering in the PDB, you might not be selecting what
you think you are. In that case you may want to use the "residue"
selection keyword instead, as it uses VMD's internal unique
residue numbering.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 10, 2009 at 09:31:26AM -0400, Alison Grinthal wrote:
> 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. 

-- 
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