VMD-L Mailing List

From: Daeun Noh (daeun.noh_at_stonybrook.edu)
Date: Thu Jun 06 2019 - 15:42:13 CDT

Hi Josh,
thanks for your reply.
I didn't understand the last parts of your explanation. If you don't mind
could you please explain more in detail?
for { set f 0 } { $f < [molinfo top get numframes] } { incr f } {
$psel frame $f
$ressel frame $f
puts "Frame $f: SASA = [measure sasa 1.4 $psel -restrict $ressel]
}

my script is in below and i got the error.
>Main< (VMD) 16 % set sel [atomselect top all]
atomselect8
>Main< (VMD) 17 % set sidechain1 [atomselect top "sidechain residue 17"]
atomselect9
>Main< (VMD) 18 % SASA=[measure sasa 1.4$sel-restrict$sidechain1]
wrong # args: should be "measure sasa <srad> <sel> [-points <varname>]
[-restrict <restrictedsel>] [-samples <numsamples>]"

On Thu, Jun 6, 2019 at 12:05 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Daeun,
>
> Measuring SASA in VMD can be done through the scripting interface,
> specifically the "measure sasa" command (
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html). I think
> you'd want to do something like this:
>
> #Select the whole protein
> set psel [atomselect top "protein"]
> #Select only the part you care about. I encourage you to visualize both of
> these selections.
> set ressel [atomselect top "sidechain and protein and resid 1"]
>
> for { set f 0 } { $f < [molinfo top get numframes] } { incr f } {
> $psel frame $f
> $ressel frame $f
> puts "Frame $f: SASA = [measure sasa 1.4 $psel -restrict $ressel]
> }
>
> -Josh
>
>
>
> On 2019-06-05 17:38:38-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Hello all,
> I am a new VMD user and now I am struggling with the program.
> I am trying to do SASA calculation of my peptide.
> Specifically, I'd like to see the SASA for the side chains of the
> specific residue not whole residue in my peptide structure but I don't know
> how to type commands.
> Are there any ways or commands to specify atom numbers to select only side
> chains and measure the SASA?
> thank you!
> Sincerely,
> Daeun
>
>