Hi Jay, We thought as much really. Well, you are going to have to use a Python script. The good news is that it's a really simple Python script. Put the following in a file whose name ends in ".py":
from chimera import openModels, Molecule
for m in openModels.list(modelTypes=[Molecule]):
from OpenSave import osOpen
f = osOpen("~/surfData/%s.data" % m.name, "w")
for a in m.atoms:
print>>f, a, getattr(a, "areaSES", 0.0)
f.close()
The indentation matters, so make sure to preserve it.
Then once you open your model and surface it, you can run the above script simply by opening it with the "open" command. It will create a file with a list of atoms and corresponding surface areas. The file will be named <model name>.data and it will be in the "surfData" folder in your home directory, so make sure that folder exists beforehand or modify the script to have it go to another location.
--Eric
On Jan 14, 2014, at 5:56 AM, "Eifler, Jay Q. (UMKC-Student)" wrote:
Actually I'm doing ab-initio quantum mechanical calculations and need
to analyze on a atom and residue basis. I've already been able to
save the atom and residue results but can't figure out how to automate
it since you have got to click buttons in the render/select attribute. The
Chimera notes seem to imply it should be possible to save attributes to
file. However, areaSAS is supposed to be an attribute but doesn't seem
to belong to the model attributes.
From: Eric Pettersen
Sent: Monday, January 13, 2014 4:05 PM
To: Eifler, Jay Q. (UMKC-Student)
Cc: <Chimera-users@cgl.ucsf.edu> List
Subject: Re: [Chimera-users] batch writing of attributes
On Jan 11, 2014, at 1:58 PM, Jay Eifler wrote:
I'm trying to automate saving the areaSAS for a bunch
of models. I've got no problem loading the models, etc.
The problem is simply how do I use command line
arguments to save the areaSAS. I've tried writesel. This
works all fine in Render/Select by attribute simply
because it has a feature to save the areaSAS to a file.
Thanks.
Hi Jay,
Do you really need the values on a per-atom basis? If you just need the grand total, it's reported in the reply log so you could just open and surface your structures one by one via a script (one by one to avoid possibly running out of memory) and then afterward save the reply log contents to a file manually (there's a "Save" button on the reply log).
--Eric
Eric Pettersen
UCSF Computer Graphics Lab