<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><div><div></div><br><div><div>On Dec 14, 2009, at 10:33 PM, Sumitro Harjanto wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div> <!-- Converted from text/rtf format --><p dir="LTR"><span lang="en-us"><font size="2" face="Book Antiqua">Hi,</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Book Antiqua">I was trying to run</font></span><span lang="en-us"><font size="2" face="Book Antiqua"> the following script</font></span><span lang="en-us"><font size="2" face="Book Antiqua"> (below)</font></span><span lang="en-us"><font size="2" face="Book Antiqua">,</font><font size="2" face="Book Antiqua"></font></span><span lang="en-us"> <font size="2" face="Book Antiqua">which calculate</font></span><span lang="en-us"><font size="2" face="Book Antiqua">s</font></span><span lang="en-us"><font size="2" face="Book Antiqua"> RMSD</font></span><span lang="en-us"><font size="2" face="Book Antiqua">s</font></span><span lang="en-us"><font size="2" face="Book Antiqua"> between 39 pdb models.</font> <font size="2" face="Book Antiqua">T</font><font size="2" face="Book Antiqua">otal</font> <font size="2" face="Book Antiqua">iteration will be 741 with about 3000 match commands.</font></span><span lang="en-us"><font size="2" face="Book Antiqua"></font> <font size="2" face="Book Antiqua">A</font><font size="2" face="Book Antiqua">fter</font> <font size="2" face="Book Antiqua">it has run for about 10 mins chimera will crash with an error:</font></span><span lang="en-us"><b> <font color="#000000" size="2" face="Arial">Chimera</font></b></span><span lang="en-us"><u><font color="#0000FF" size="2" face="Arial"> </font></u></span><span lang="en-us"><font color="#000000" size="2" face="Arial">failed abnormally; the exit code was 3</font></span><span lang="en-us"><font color="#000000" size="2" face="Arial">.</font> <font color="#000000" size="2" face="Arial">I</font><font color="#000000" size="2" face="Arial">'ve printed the debug lines below the script:</font></span><span lang="en-us"></span></p><p dir="LTR"><span lang="en-us"><font color="#000000" size="2" face="Arial">Any suggestions..?</font></span></p><p dir="LTR"><span lang="en-us"><font color="#000000" size="2" face="Arial">Cheers,</font></span></p><p dir="LTR"><span lang="en-us"><font color="#000000" size="2" face="Arial">Sumitro</font></span><span lang="en-us"></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">--------------------------------------------------------</font></span><span lang="en-us"></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">open d:\result\pdb\1B0G.pdb</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">open d:\result\pdb\1DUZ.pdb</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-9.C@ca #1:1-9.C@ca</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-2.C,8-9.C@n,ca,c,o #1</font><font size="2" face="Courier New">:1-2.C,8-9.C@n,ca,c,o</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">close #1</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">open d:\result\pdb\1EEY.pdb</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-9.C@ca #1:1-9.C@ca</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">close #1</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">open d:\result\pdb\</font><font size="2" face="Courier New">1EEZ.pdb</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-9.C@ca #1:1-9.C@ca</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">close #1</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">open d:\result\pdb\1HHG.pdb</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-9.C@ca #1:1-9.C@ca</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">close #1</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">open d:\result\pdb\1HHI.pdb</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-9.C@ca #1:1-9.C@ca</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-9.C@n,ca,c,o #1:1-9.C@n,ca,c,o</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0</font><font size="2" face="Courier New">:1-2.C,8-9.C@ca #1:1-2.C,8-9.C@ca</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">match #0:1-2.C,8-9.C@n,ca,c,o #1:1-2.C,8-9.C@n,ca,c,o</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">close #1</font></span><span lang="en-us"></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">…</font></span><span lang="en-us"></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">…</font></span><span lang="en-us"></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">…</font></span><span lang="en-us"></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">--------------------------------------------------------</font></span><span lang="en-us"></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">initializing general preferences</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">loading Tix</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">initializing graphics</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">create application</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">loading Pmw</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">creating main window</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">creating menus</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">creating toolbar</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">creatin</font><font size="2" face="Courier New">g viewer</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">initializing OpenGL</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">initializing preferences</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">initializing dialogs</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">initializing COM</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">initializing extensions</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">CloneMenu failed inside of MenuAddOrInsert.</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">This application has requested the Runtime to terminate it in an unusual way.</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">Please contact th</font><font size="2" face="Courier New">e application's support team for more information.</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">Return code: 3</font></span></p><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">Press return or enter to to exit</font></span><span lang="en-us"></span></p><div><span lang="en-us"></span><br class="webkit-block-placeholder"></div><p dir="LTR"><span lang="en-us"><font size="2" face="Courier New">-------------------------------------------------------</font><font size="2" face="Courier New">-</font></span><span lang="en-us"></span></p><div><span lang="en-us"></span><br class="webkit-block-placeholder"></div> </div> _______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br></div></div></div></body></html>