VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 10 2009 - 13:31:54 CDT

Alison,
  What do you get from this:
set rmsf [measure rmsf $sel first 1 last 3991 step 10]
llength $rmsf

Cheers,
  John

On Fri, Jul 10, 2009 at 02:10:14PM -0400, Alison Grinthal wrote:
> Thanks - I checked and $sel num does give 288. One thing I noticed is that
> in the output file, the rmsf for the 223rd residue often has fewer digits
> than the other rmsf's, as if it was interrupted. I'm not sure
> what could be doing that, but if you have any more suggestions of what to
> look at to detect sources of problems, please let me know. Thanks again.
>
> On Fri, 10 Jul 2009, John Stone wrote:
>
> >
> >Hi,
> > What do you get if you do this:
> >set sel [atomselect top "resid 1 to 288 and name CA"]
> >$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
> > 

-- 
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