VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 15 2009 - 16:03:25 CDT

Hi,
  Your -restrict selection is indeed changing with time, because
you are calling "$sel frame $i" immediately prior to computing the SASA.
You can visually determine if you're getting surface area you think you're
measuring through the use of the -points option, and plotting the
resulting list of points. Please see the VMD User's Guide for more
information on "measure sasa":
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 10, 2009 at 09:12:23PM +0800, yzliu wrote:
> Dear all:
>
> The SASA of a atomselect could be calculated by the "measure"
> command in VMD as follow:
> "measure sasa srad selection [-restrict restrictedsel] "
> I do not understand what is the meaning of '-restrict' option exactly.
> In my vmd srcipt as follow, the SASA with the "-restrict"is invariable
> as a funtion of time.
>
> set nf [molinfo top get numframes]
> set all [atomselect top all]
> set sel [atomselect top "resid 1 and segname DMPC"]
>
> for {set i 0} {$i < $nf} {incr i} {
> $sel frame $i
> set sasa [measure sasa 1.4 $all -restrict $sel]
> puts $sasa
> }
> I do not know whether there is someting wrong in the script. However,
> when
> I use "measure sasa 1.4 $sel ", the SASA is changed as evolution.
> In my opinion, without "-restrict" means calculating SASA of a isolated
> molecule
> in the solvent.Wiht "-restrict" means calculating SASA of a molecule in
> the
> real environment. The diffierent circumstance would influence the SASA.
>
> I am not sure whether my understanding is right.
> Any information will be appreciaed
>
> Best Regards,
>
> Yingzhe
>
> --
> ==============================
> Yingzhe Liu
> PHD Student of Analytical Chemistry
> Chemistry Department
> Nankai University
> Tianjin, P.R.China,30071
> Email: nk.liuyz_at_gmail.com
> ============================== 

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