VMD-L Mailing List

From: Alison Grinthal (agrinth_at_fas.harvard.edu)
Date: Fri Jul 10 2009 - 13:10:14 CDT

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
>