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<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>>chimera --nogui open
e:\A.Model_receptor\model_env\calc_receptor_rmsds.cmd<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>But again I got the same error message:<br>
***********************************************************************<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p>************************************************************************<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Below is what I see after adding
"--debug" to the command:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>***********************************************************************<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>ValueError: Unknown model type<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Error while processing open:</span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p>ValueError: Unknown model type<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>See reply log for Phyton traceback.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Opening 2HN7.pdb…<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>1 model opened<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Opened … … … (and
actually continues to complete my script)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>***********************************************************************<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>*********************************************************************<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>{'Model Panel':
{'freqButs': {'2D Diagram': False,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'activate': False,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'activate all': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'activate only': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'add hydrogens...': False,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'add/edit note...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'attributes...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'blast protein...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'clipping...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'close': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'color by SS...': False,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'compute SS': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'copy/combine...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'deactivate': False,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'focus': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'hide': False,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'match...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'minimize...': False,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'rainbow...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'rename...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'render/sel
by attr...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'select': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'select chain(s)...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'sequence...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'show': False,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'show
all atoms': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'show only': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'surface main': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'tile...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'toggle active': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'trace
backbones': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'trace chains': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'transform as...': True,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'write PDB': True},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'lastUse': 1268231127.7550001},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'> 'Nucleotides':
{'slab styles': {}},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'> 'Ribbon
Styles': {'atoms': {}, 'scaling': {}, 'xsections': {}},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'> 'Tools':
{'autoStart': {},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'confirmOnStart': {},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'dirList': [],<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'inFavorites': {'Command Line': 2,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'Model Panel': 0,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'Reply Log': 4,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'Sequence': 3,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'Side View': 1},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'onToolbar': {}},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'> 'command
line gui': {'remembered commands': ['select #0:2-182.A@C', <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'write selected format pdb 0 E:\\A.Model_receptor\\PDB_MODELS\\1W72_c.pdb']},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'> 'initial
size': {'Window size': (525, 513)},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'> 'miller
browser': {'dirHistory': [u'E:\\A.Model_receptor\\Chimera_log_parser', <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'C:\\Users\\wiason\\Desktop'],<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'fileHistory': {'': [u'E:\\A.Model_receptor\\Chimera_log_parser\\RMSD_raw.txt',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'E:\\A.Model_receptor\\PDB_MODELS\\peptide_chain\\reply_log',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'C:\\Users\\wiason\\Desktop\\try_combining2.pdb',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'C:\\Users\\wiason\\Desktop\\try_combining.pdb'],<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;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></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'E:\\A.Model_receptor\\PDB_MODELS\\peptide_chain\\extract_peptide_from_PDB.cmd',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'E:\\A.Model_receptor\\PDB_MODELS\\3D39.pdb',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'E:\\A.Model_receptor\\PDB_MODELS\\3D39.fasta',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'E:\\A.Model_receptor\\PDB_MODELS\\3DTX.pdb',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'E:\\A.Model_receptor\\PDB_MODELS\\3B3I.pdb',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'E:\\A.Model_receptor\\PDB_MODELS\\2JCC.pdb',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'E:\\A.Model_receptor\\PDB_MODELS\\2J8U.pdb',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'E:\\A.Model_receptor\\PDB_MODELS\\1LP9.pdb',<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
u'E:\\A.Model_receptor\\PDB_MODELS\\1B0G.pdb']},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'>
'lastFilter': {'main chimera import dialog': 'all (guess type)'}},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'> 'update
check': {'last time': (2010, 3, 3, 12, 50, 48, 371000, None)},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'> 'version
tracking': {'last version': '1.4_b29093'},<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'> 'write PDB
dialog': {'multiSavePDB': 'single'}}<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>****************************************************************************************************<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span lang=EN-US
style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span lang=EN-US style='font-size:10.0pt;font-family:Tahoma'>
Eric Pettersen [mailto:pett@cgl.ucsf.edu] <br>
<b><span style='font-weight:bold'>Sent:</span></b> 10 March 2010 3:17 AM<br>
<b><span style='font-weight:bold'>To:</span></b> Sumitro Harjanto<br>
<b><span style='font-weight:bold'>Cc:</span></b> chimera-users@cgl.ucsf.edu<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Chimera-users]
Scripting to write / save multiple models into single pdf file</span></font><span
lang=EN-US><o:p></o:p></span></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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 <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></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>--Eric <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</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>
<p class=MsoNormal><font size=3 color=black face=Helvetica><span
style='font-size:12.0pt;font-family:Helvetica;color:black'>
Eric
Pettersen<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 color=black face=Helvetica><span
style='font-size:12.0pt;font-family:Helvetica;color:black'>
UCSF
Computer Graphics Lab<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 color=black face=Helvetica><span
style='font-size:12.0pt;font-family:Helvetica;color:black'>
<a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 color=black face=Helvetica><span
style='font-size:12.0pt;font-family:Helvetica;color:black'><o:p> </o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Mar 8, 2010, at 7:32 PM, Sumitro Harjanto wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
</span><span style='orphans: 2;text-align:auto;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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> <u1:p></u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>-----------------------------------------------------------------------------------------------------<u1:p></u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>--------------------------------------------------------------------------------------------------<u1:p></u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;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></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
</div>
</div>
</div>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</span></u1:smarttagtype></div>
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