<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Sumitro,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Don't include "open" on the Unix command line. You only need that when typing into Chimera's own command line.</div><div><br></div><div>--Eric</div><div><br><div><div>On Mar 10, 2010, at 10:28 AM, Sumitro Harjanto wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div lang="EN-SG" link="blue" vlink="blue" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">That was a bull’s eye, indeed, after turning off the autostart for Model panel, the simple command of “>chimera --nogui” does not make anymore complain.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">So I advanced a little and try to run a .cmd file using the command prompt:<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">>chimera --nogui open e:\A.Model_receptor\model_env\calc_receptor_rmsds.cmd<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">But again I got the same error message:<br>***********************************************************************<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Chimera failed abnormally; the exit code was: 1</span></font><font color="black"><span style="color: black; "><u1:p></u1:p><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Use –debug command line option for the full error message.<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><u1:p>************************************************************************<o:p></o:p></u1:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Below is what I see after adding "--debug" to the command:<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">***********************************************************************<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Cannot execute 'gzip': no automatic decompression of .Z files<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Traceback (most recent call last):<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimeraInit.py", line 425, in init</span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> Chimera.openModels.open<a, prefixableType=1></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\__init__.py", line 1405, in open</span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> Raise ValueError, "Unknown model type"</span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">ValueError: Unknown model type<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Error while processing open:</span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><u1:p>ValueError: Unknown model type<o:p></o:p></u1:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\__init__.py", line 1405, in open</span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> Raise ValueError, "Unknown model type"</span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">See reply log for Phyton traceback.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Opening 2HN7.pdb…<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">1 model opened<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Opened … … … (and actually continues to complete my script)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">***********************************************************************<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Later on I tried to open a pdb instead (>chimera --nogui open e:\A.Model_receptor\PDB_MODELS\3B3I.pdb) and the same thing happened, even the debug window shows the same message about unknown model type.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Any way to go around this..? I don’t know if it helps, but below is my “preferences” file<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">*********************************************************************<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; ">{'Model Panel': {'freqButs': {'2D Diagram': False,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'activate': False,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'activate all': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'activate only': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'add hydrogens...': False,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'add/edit note...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'attributes...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'blast protein...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'clipping...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'close': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'color by SS...': False,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'compute SS': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'copy/combine...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'deactivate': False,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'focus': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'hide': False,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'match...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'minimize...': False,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'rainbow...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'rename...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'render/sel by attr...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'select': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'select chain(s)...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'sequence...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'show': False,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'show all atoms': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'show only': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'surface main': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'tile...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'toggle active': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'trace backbones': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'trace chains': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'transform as...': True,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'write PDB': True},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'lastUse': 1268231127.7550001},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'Nucleotides': {'slab styles': {}},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'Ribbon Styles': {'atoms': {}, 'scaling': {}, 'xsections': {}},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'Tools': {'autoStart': {},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'confirmOnStart': {},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'dirList': [],<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'inFavorites': {'Command Line': 2,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'Model Panel': 0,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'Reply Log': 4,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'Sequence': 3,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'Side View': 1},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'onToolbar': {}},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'command line gui': {'remembered commands': ['select #0:2-182.A@C',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'write selected format pdb 0 E:\\A.Model_receptor\\PDB_MODELS\\1W72_c.pdb']},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'initial size': {'Window size': (525, 513)},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'miller browser': {'dirHistory': [u'E:\\A.Model_receptor\\Chimera_log_parser',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'C:\\Users\\wiason\\Desktop'],<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'fileHistory': {'': [u'E:\\A.Model_receptor\\Chimera_log_parser\\RMSD_raw.txt',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'E:\\A.Model_receptor\\PDB_MODELS\\peptide_chain\\reply_log',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'C:\\Users\\wiason\\Desktop\\try_combining2.pdb',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'C:\\Users\\wiason\\Desktop\\try_combining.pdb'],<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'main chimera import dialog': [u'E:\\A.Model_receptor\\model_env\\calc_receptor_rmsds.cmd',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'E:\\A.Model_receptor\\PDB_MODELS\\peptide_chain\\extract_peptide_from_PDB.cmd',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'E:\\A.Model_receptor\\PDB_MODELS\\3D39.pdb',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'E:\\A.Model_receptor\\PDB_MODELS\\3D39.fasta',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'E:\\A.Model_receptor\\PDB_MODELS\\3DTX.pdb',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'E:\\A.Model_receptor\\PDB_MODELS\\3B3I.pdb',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'E:\\A.Model_receptor\\PDB_MODELS\\2JCC.pdb',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'E:\\A.Model_receptor\\PDB_MODELS\\2J8U.pdb',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'E:\\A.Model_receptor\\PDB_MODELS\\1LP9.pdb',<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> u'E:\\A.Model_receptor\\PDB_MODELS\\1B0G.pdb']},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'lastFilter': {'main chimera import dialog': 'all (guess type)'}},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'update check': {'last time': (2010, 3, 3, 12, 50, 48, 371000, None)},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'version tracking': {'last version': '1.4_b29093'},<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "> 'write PDB dialog': {'multiSavePDB': 'single'}}<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span lang="EN-US" style="font-size: 11pt; font-family: 'Courier New'; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">****************************************************************************************************<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN-GB" style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div><div class="MsoNormal" align="center" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; text-align: center; "><font size="3" face="Times New Roman"><span lang="EN-US" style="font-size: 12pt; "><hr size="2" width="100%" align="center" tabindex="-1"></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><b><font size="2" face="Tahoma"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma; font-weight: bold; ">From:</span></font></b><font size="2" face="Tahoma"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma; "><span class="Apple-converted-space"> </span>Eric Pettersen [<a href="mailto:pett@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">mailto:pett@cgl.ucsf.edu</a>]<span class="Apple-converted-space"> </span><br><b><span style="font-weight: bold; ">Sent:</span></b><span class="Apple-converted-space"> </span>10 March 2010 3:17 AM<br><b><span style="font-weight: bold; ">To:</span></b><span class="Apple-converted-space"> </span>Sumitro Harjanto<br><b><span style="font-weight: bold; ">Cc:</span></b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">chimera-users@cgl.ucsf.edu</a><br><b><span style="font-weight: bold; ">Subject:</span></b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Scripting to write / save multiple models into single pdf file</span></font><span lang="EN-US"><o:p></o:p></span></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span lang="EN-GB" style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">Hmm, it seems that you have the Model Panel set to autostart in your preferences. Now, Chimera probably should ignore autostarting tools when it is in nogui mode, but currently it doesn't. So what you will have to do for now (until we fix this) is to start Chimera normally, turn off the autostart of the Model Panel (and any other graphical tools probably), save the new preferences, and then run your script.<o:p></o:p></span></font></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">If you look in the "Preferences" preference category, it will show the location of the preferences file. You could squirrel away your original preferences file somewhere, make the version with no autostarting, copy<span class="Apple-converted-space"> </span><i><span style="font-style: italic; ">that</span></i> somewhere, and then put your original version back. You would then be able to use the no-autostarting preferences by specifying it's location with the --preferences startup option.<o:p></o:p></span></font></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">--Eric <o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div></div><div><span style="-webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; orphans: 2; widows: 2; word-spacing: 0px; "><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" color="black" face="Helvetica"><span style="font-size: 12pt; font-family: Helvetica; color: black; "> Eric Pettersen<o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" color="black" face="Helvetica"><span style="font-size: 12pt; font-family: Helvetica; color: black; "> UCSF Computer Graphics Lab<o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" color="black" face="Helvetica"><span style="font-size: 12pt; font-family: Helvetica; color: black; "> <a href="http://www.cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">http://www.cgl.ucsf.edu</a><o:p></o:p></span></font></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" color="black" face="Helvetica"><span style="font-size: 12pt; font-family: Helvetica; color: black; "><o:p> </o:p></span></font></div></div></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">On Mar 8, 2010, at 7:32 PM, Sumitro Harjanto wrote:<o:p></o:p></span></font></div></div><p class="MsoNormal" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 12pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></p><span style="orphans: 2; widows: 2; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; word-spacing: 0px; "><u1:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PersonName"><div link="blue" vlink="blue" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Hi Eric,<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><u1:p> </u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Thanks for the suggestion. I don’t really script, I usually use a c++ code / excel to generate the command (.cmd) files. Should be okay for the automation for now, if I run into any problem then I will post it up here again. =]<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> <u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Mean while I try running the command “chimera.exe –nogui” in PATH/chimera/bin but got the following error message. I followed the instruction and copy over the debug message (below). any advise? I’m on a win7 X86 platform btw.<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><u1:p> </u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Thanks,<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Sumitro<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><u1:p> </u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">-----------------------------------------------------------------------------------------------------<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><u1:p> </u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Chimera failed abnormally; the exit code was: 1</span></font><font color="black"><span style="color: black; "><u1:p></u1:p><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Use –debug command line option for the full error message.<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><u1:p> </u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">--------------------------------------------------------------------------------------------------<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Cannot execute 'gzip': no automatic decompression of .Z files<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Traceback (most recent call last):<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\__main__.py", line 65, in <module><u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> value = chimeraInit.init(sys.argv)<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimeraInit.py", line 401, in init<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> extension.startup(startExtensions)<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\extension\base.py", line 1056, in startup<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> manager.autostartTools(extNames)<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\extension\base.py", line 959, in autostartTools<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><u1:p> </u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> emo.activate()<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\ModelPanel\ChimeraExtension.py", line 23, in activate<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> display(self.module('base').ModelPanel.name)<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\dialogs.py", line 77, in display<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> dialog = find(name, create=1)<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\dialogs.py", line 62, in find<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> return d()<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\baseDialog.py", line 523, in __init__<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> BaseDialog.__init__(self, master, *args, **kw)<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\chimera\baseDialog.py", line 244, in __init__<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> self.fillInUI(self.__top)<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\ModelPanel\base.py", line 217, in fillInUI<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> self._addColumns()<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\ModelPanel\base.py", line 436, in _addColumns<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> self._buildTable()<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\share\ModelPanel\base.py", line 454, in _buildTable<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> % len(filter(lambda s: s == 1, self.shownColumns)))<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 1306, in __init__<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> cnf, kw)<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 307, in __init__<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "> self.tk.call(widgetName, self._w, *extra)<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">_tkinter.TclError: invalid command name "tixScrolledHList"<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Return code: 1<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Press return or enter to to exit<u1:p></u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><u1:p> </u1:p></span></font><font color="black"><span style="color: black; "><o:p></o:p></span></font></div></div></div></div></u1:smarttagtype></span></div></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div></div></div></div></span></blockquote></div><br></div></body></html>