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Hi Ryan,<div><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>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:</div><div><br class="webkit-block-placeholder"></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>from sys import __stderr__ as stderr</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>print>>stderr, "OUTPUT", "my result:", r</div><div><br class="webkit-block-placeholder"></div><div>and run Chimera with:</div><div><br class="webkit-block-placeholder"></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>chimera --nogui myscript.py |& grep OUTPUT</div><div><br class="webkit-block-placeholder"></div><div>--Eric</div><div><br><div><div>On Jan 8, 2008, at 12:19 PM, Ryan Pavlovicz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">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.? <br><br><div class="gmail_quote">On Jan 8, 2008 1:24 PM, Eric Pettersen < <a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style=""> Well to suppress all output you would use normal shell redirection to /dev/null. For csh-style shells, something like this:<div><br></div><div><span style="white-space: pre;"> </span>chimera --nogui >& /dev/null</div> <div><br></div><div>--Eric</div><div><br><div> <span style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 16px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="5"> <span> <span> </span></span>Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 16px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="5"> <span> <span> </span></span>UCSF Computer Graphics Lab</font></div><div class="Ih2E3d"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 16px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="5"> <span> </span><a href="http://www.cgl.ucsf.edu" target="_blank">http://www.cgl.ucsf.edu</a></font></div><br></div></span> </div><br><div><div>On Jan 8, 2008, at 9:28 AM, Ryan wrote:</div><br><blockquote type="cite"> <div style="margin: 0px;">The --nostatus option will suppress messages like: <span> </span></div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;"><span> </span>"Executing xxx.py... Opening xxx.pdb..."</div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;">but still, messages like:</div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;"><span> </span>"Model 0 (xxx.pdb) appears to be a protein with noe secondary structure assignements.<span> </span>Computing assignments..." & "warning:<span> </span>duplicate atom serial number found..." </div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;">are still printed to the screen.<span> </span>Are there ways to suppress these messages as well?<span> </span>Thanks again,</div><div style="margin: 0px; min-height: 14px;"> <br></div><div style="margin: 0px;">ryan</div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;">_______________________________________________ </div><div style="margin: 0px;">Chimera-users mailing list</div><div style="margin: 0px;"><a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a></div><div style="margin: 0px;"><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank"> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div> </blockquote></div><br></div></div></blockquote></div><br></blockquote></div><br></div></body></html>