From: Peter Hains (
Date: Thu Jan 18 2007 - 15:34:16 CST

Hi John,

thanks for the help with MSMS, I've got that working. I cannot seem
to work out the exact sequence to get "sasa" working for me. I have
looked over the mailing list archive, but I can't find anything that
answers my questions.

What I want to do is determine the surface accessible area for a
number of residues in a given PDB file.

I can work out I need to use "measure sasa srad ...." but I'm unclear
on the exact options/requirements. Do I need to use "atomselect" in
the same command, or do I select the atoms first and then use the
"atomselect0" to use that selection with the measure command?

If you could just give me an example command I should be able to work
it out from there.

Thanks again,


>For measuring solvent accessible surface area, you'll
>want to use the "measure sasa" command. There isn't a
>graphical interface for this yet, since there are so many
>ways to use this command, but there are a number of past emails
>on this subject in the VMD-L archive that you can reference to
>help you get started. Let us know if you have more questions
>on this.