buriedarea and sasa should exclude ions, solvent, ligands

[Tom Goddard]

Should the buriedarea and sasa (solvent accessible surface area) exclude ions, solvent and ligands from atom specs unless an option saying to include them is given?

Begin forwarded message:

From: Elaine Meng
Subject: Re: buriedarea command options
Date: September 14, 2016 at 6:40:22 PM PDT
To: Tom Goddard

Hmm, I’m really not sure. It would make the command more complicated, but then again, make it more likely for people who don’t read the documentation to get what they think they’re getting.

Let’s see, how complicated would it have to be…
The default could be to ignore non-biopolymer atoms unless an atomspec contains only non-biopolymer atoms. Would that then take both atomspecs literally or just the one with only non-biopolymer atoms? E.g. 4hhb “:hem with ~:hem”, should the latter include solvent? Then on top of that, there could be some keyword, say “allAtoms” that would enforce taking both atomspecs literally no matter what they contained, as long as they were nonoverlapping.

Hmm, I”m still feeling wishy-washy about it… either way is OK with me.
Elaine