<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">What version of Chimera are you running?<div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </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> 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