VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri Sep 18 2015 - 11:51:03 CDT

Hi Josh,

Thank you so much for the explanation. That really helps a lot.

Best,
Chitrak.

On Thu, Sep 17, 2015 at 9:27 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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.
>
>
>