Cheong Wee Loong, Daniel wrote:
Thanks for the explanation. It is much clearer now. Although I
still don't quite understand why we can't just use Protein A as the
calculation group AND output group to find the SASA of protein A.
If A is complexed to B in solvent you might want the true SASA of
protein A (since B is not solvent, A's surface with B is not part of the
SASA), or maybe the SASA of A while pretending that B was solvent, or
indeed something else.
I
know it states that the calculation group should be all non-solvent
atoms, but I guess I am just trying to understand why. As in why do
we need both the calculation and output groups in the first place?
Why can't we just use the group of atoms that we are want to find the
SASA for?
You can - just specify the same group twice. Your suggestion would save
a negligible amount of effort for such simple usage, and leave no
available solution for more complex usage.
Justin's example was a good one. The use of two different index groups
allows the user total control over the form of the calculation. This is
how software should work. As a programmer, you can't anticipate all
possible usage patterns, and so making available a general and flexible
user interface is usually best when most of your users will have
suitable expertise to use it. At the same time, you shouldn't make life
difficult for simple usage.
Mark
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