[Chimera-users] Calculating SAS areas for selected residues for a whole trajectory of structures

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 24 11:52:45 PDT 2013

Hi Harald,
	I think you'll need a Python script to do this.  The script is pretty simple and I've attached it to this mail.  To use the script, in the Per-Frame menu of MD Movie choose Define Script.  Then make sure the "Interpret script as" option is set to Python.  You can then read the script into the Script window with the "Insert text file…" button.  Choose OK or Apply to have the script executed when you run your trajectory.  It will send output to the reply log.  Make sure you've created the surface you want and selected the residues of interest.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Sep 24, 2013, at 7:31 AM, Harald Lanig <harald.lanig at fau.de> wrote:

> Dear Chimera users,
> I am currently using chimera to calculate the solvent accessible surface for several selected residues of a single structure (I am using the Attribute calculator with the formula sum(atom.areaSAS) to do this).
> Is there a way to apply this to a set of structures coming from a molecular dynamics trajectory? I am interested in how the solvent accessible surface of a set of residues changes during the simulation.
> Any hint is highly appreciated!
> Best wishes,
> -Harald

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