[Chimera-users] Surface area list

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 28 09:28:15 PDT 2016

Hi Lothar,
You can use a script with commands and then save the results from the Reply Log.

More details...
As soon as you calculate and show molecular surfaces, for example with the “surface” command, the analytical surface areas are reported in the Reply Log (open from Favorites menu).   Similarly, if you use “measure area” and “measure volume” commands, the values will be in the Reply Log.  The surface areas from “measure area” will be a little different than from the “surface” command, because the former just sums up the flat surface triangle areas rather than figuring out the analytical (curved) surface area like the latter.  If you had used “split”, the surfaces would be in separate submodels but with the same main model number, e.g. #0.1, #0.2, etc., but you could just measure them en masse, e.g. command

measure volume #0

They would still be listed separately in the Reply Log.  

Now, to loop through multiple structures, you may want to embed the Chimera commands in a Python script instead of just making a Chimera command script.  How to do that is outlined here:

Saving the Reply Log contents to file:

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 28, 2016, at 9:09 AM, esserlo at helix.nih.gov wrote:
> Hi,
>  with the help of "split #0" I created 10 segments of my protein and
> calculated the surface of each fragment. I can go to tools and measure
> volume and area but I'd prefer to write out the results as a file. Can
> Chimera do this ?
> I am asking because I intend to do more complex things than just 10 surfaces
> and it would be rather tedious if not impossible to do all this by hand.
> Thanks for any advice.
> Lothar

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