VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Sep 17 2015 - 09:27:36 CDT

Hi Chitrak,

It helps here to think about what the code is actually doing behind the
scenes. For the given atomselection, it picks 500 random points around
each atom that are the radius + 1.4A (for the water molecule) away from
the center of the atom. If the point winds up being inside another atom
in the selection, the point is excluded, but if not, it is considered to
be on the surface. What the restrict option does is decouples the two
lists of atoms. The first selection is for the inside/outside check, and
the "restrict" option is to only count the surface area for specific
parts of the whole.

In your case, without restrict, the surface being considered is the
entire surface of residue 5 (including surface area that would be buried
by the rest of the protein). With restrict, you are now calculating the
surface of residue 5 that isn't buried by the proteins.

-Josh Vermaas

On 09/16/2015 12:42 PM, Chitrak Gupta wrote:
> Dear VMD users,
>
> I have a confusion regarding the "measure sasa" command in VMD. I went
> through the mailing list, but nobody seems to have answered the
> specific question.
>
> I am interested in measuring the sasa of individual residues of my
> protein. My question is, if I want to measure the sasa of say residue
> 5 (set residue5 [atomselect top "protein and residue 5"]), what is the
> difference between the following two commands?
>
> measure sasa 1.4 $residue5
>
> measure sasa 1.4 $protein -restrict $residue5
>
>
> I have found that the former usually gives a higher value. I have also
> tried using the -points option to view the SASA sample points, and
> even there I see the former has a slightly larger volume.
>
> What I want to know is, what gives rise to this difference? What am I
> measuring in these two cases?
>
>
> Best regards,
> Chitrak.