Hi Ryan,
Perhaps other Chimera developers can chime in, but I don't know of any good way to selectively suppress the non-status messages that Chimera generates, particularly the "duplicate atom serial number" messages which are being put on standard error by code in the C++ layer.
What I can suggest in your situation is that you have your print statements go to standard error (so that they flush through pipes immediately) and that you prefix them with some unique string that you can grep for.  Something like:

from sys import __stderr__ as stderr
print>>stderr, "OUTPUT", "my result:", r

and run Chimera with:

chimera --nogui myscript.py |& grep OUTPUT

--Eric

On Jan 8, 2008, at 12:19 PM, Ryan Pavlovicz wrote:

Are there ways just to suppress the chimera output?  I'd still like to see some of my print commands that are part of my python script, so i can easily debug, follow a process, etc.?

On Jan 8, 2008 1:24 PM, Eric Pettersen < pett@cgl.ucsf.edu> wrote:
Well to suppress all output you would use normal shell redirection to /dev/null.  For csh-style shells, something like this:

chimera --nogui >& /dev/null

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 8, 2008, at 9:28 AM, Ryan wrote:

The --nostatus option will suppress messages like:  

   "Executing xxx.py... Opening xxx.pdb..."

but still, messages like:

   "Model 0 (xxx.pdb) appears to be a protein with noe secondary structure assignements.  Computing assignments..." & "warning:  duplicate atom serial number found..."

are still printed to the screen.  Are there ways to suppress these messages as well?  Thanks again,

ryan


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