[Chimera-users] Surface area list

esserlo at helix.nih.gov esserlo at helix.nih.gov
Wed Sep 28 14:59:08 PDT 2016

Hi Elaine,

> 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.

  This is very helpfu. I did not realize that there is a Reply Log as such.

> 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:
> <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

  Well, I am very fuzzy with Python - I am more tcl guy. But I think with
simple command scripts I can do it followed copy and paste of the log file,
I can in the end write a program to sort the log file for the entries and
values I need.


Have a great day.


> Saving the Reply Log contents to file:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-September/000924.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-July/005367.html>
> I hope this helps,
> Elaine
> ----------
> 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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