VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Sep 16 2015 - 12:42:26 CDT

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.