<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PersonName"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"\@SimSun";
panose-1:2 1 6 0 3 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:595.3pt 841.9pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.Section1
{page:Section1;}
-->
</style>
</head>
<body 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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Ok Eric, I think you can ignore my last
email. I realised I can use “chimera –nogui –debug” to
make the chimera command line appear and then I can open my .cmd file from
there. But I realised also I cant save the reply log, which contain the rmsd
information I need (my result!! T.T) <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'>I found this codet on the chimera mailing
list:<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 color=navy
face=Arial><span lang=EN style='font-size:10.0pt;font-family:Arial;color:navy'>def
save_reply_log(path):<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 color=navy
face=Arial><span lang=EN style='font-size:10.0pt;font-family:Arial;color:navy'>
from chimera import dialogs<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 color=navy
face=Arial><span lang=EN style='font-size:10.0pt;font-family:Arial;color:navy'>
r = dialogs.find('reply')<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 color=navy
face=Arial><span lang=EN style='font-size:10.0pt;font-family:Arial;color:navy'>
text = r.text.get('1.0', 'end')<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 color=navy
face=Arial><span lang=EN style='font-size:10.0pt;font-family:Arial;color:navy'>
f = open(path, 'w')<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 color=navy
face=Arial><span lang=EN style='font-size:10.0pt;font-family:Arial;color:navy'>
f.write(text)<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 color=navy
face=Arial><span lang=EN style='font-size:10.0pt;font-family:Arial;color:navy'>
f.close()<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 color=navy
face=Arial><span lang=EN style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 color=navy
face=Arial><span lang=EN style='font-size:10.0pt;font-family:Arial;color:navy'>save_reply_log("/tmp/tmplog.txt")<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN
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
style='font-size:10.0pt;font-family:Arial;color:navy'>but how do I incorporate
this into my .cmd..? or must I now script in python..?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN
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
style='font-size:10.0pt;font-family:Arial;color:navy'>thanks!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN
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
style='font-size:10.0pt;font-family:Arial;color:navy'>Cheers,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN
style='font-size:10.0pt;font-family:Arial;color:navy'>Sumitr.<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>
<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> 12 March 2010 6:24 AM<br>
<b><span style='font-weight:bold'>To:</span></b> Sumitro Harjanto<br>
<b><span style='font-weight:bold'>Cc:</span></b> <st1:PersonName w:st="on">chimera-users@cgl.ucsf.edu</st1:PersonName><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 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'>Hi Sumitro,<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><span class=apple-tab-span><font size=3
face="Times New Roman"><span style='font-size:12.0pt'> </span></font></span>Don't
include "open" on the Unix command line. You only need that
when typing into Chimera's own command line.<o:p></o:p></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>
<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>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Mar 10, 2010, at 10:28 AM, Sumitro Harjanto wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br>
<o:p></o:p></span></font></p>
<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'>
<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'>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.<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'>So I advanced a little and try to run a
.cmd file using the command prompt:<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 --nogui open
e:\A.Model_receptor\model_env\calc_receptor_rmsds.cmd<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'>But again I got the same error message:<br>
***********************************************************************<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'><u2:p></u2:p><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.<u2:p></u2:p></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'><u2:p>************************************************************************<u1:p></u1:p></u2: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'>Below is what I see after adding
"--debug" to the command:<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<u2:p></u2:p></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'>Traceback (most recent call last):<u2:p></u2:p></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'> File
"E:\Chimera\share\chimeraInit.py", line 425, in init</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'> Chimera.openModels.open<a,
prefixableType=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'> File
"E:\Chimera\share\chimera\__init__.py", line 1405, in open</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'> Raise ValueError,
"Unknown model type"</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'>ValueError: Unknown model type<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'>Error while processing open:</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'><u2:p>ValueError: Unknown model type<u1:p></u1:p></u2: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'> File
"E:\Chimera\share\chimera\__init__.py", line 1405, in open</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'> Raise ValueError,
"Unknown model type"</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'><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'>See reply log for Phyton traceback.<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'>Opening 2HN7.pdb…<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'>1 model opened<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'>Opened … … … (and
actually continues to complete my script)<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'>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.<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'>Any way to go around this..? I don’t
know if it helps, but below is my “preferences” file<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>{'Model
Panel': {'freqButs': {'2D Diagram': False,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'activate': False,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'activate all': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'activate only': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'add hydrogens...': False,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'add/edit note...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'attributes...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'blast protein...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'clipping...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'close': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'color by SS...': False,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'compute SS': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'copy/combine...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'deactivate': False,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'focus': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'hide': False,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'match...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'minimize...': False,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'rainbow...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'rename...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'render/sel
by attr...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'select': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'select chain(s)...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'sequence...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'show': False,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'show
all atoms': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'show only': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'surface main': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'tile...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'toggle active': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'trace
backbones': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'trace chains': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'transform as...': True,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'write PDB': True},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'lastUse': 1268231127.7550001},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'> 'Nucleotides':
{'slab styles': {}},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'> 'Ribbon
Styles': {'atoms': {}, 'scaling': {}, 'xsections': {}},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'> 'Tools':
{'autoStart': {},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'confirmOnStart': {},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'dirList': [],<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'inFavorites': {'Command Line': 2,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'Model Panel': 0,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'Reply Log': 4,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'Sequence': 3,<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'Side View': 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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'onToolbar': {}},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'> 'command
line gui': {'remembered commands': ['select #0:2-182.A@C',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'write selected format pdb 0 E:\\A.Model_receptor\\PDB_MODELS\\1W72_c.pdb']},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'> 'initial
size': {'Window size': (525, 513)},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'> 'miller
browser': {'dirHistory': [u'E:\\A.Model_receptor\\Chimera_log_parser',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'C:\\Users\\wiason\\Desktop'],<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'fileHistory': {'': [u'E:\\A.Model_receptor\\Chimera_log_parser\\RMSD_raw.txt',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'E:\\A.Model_receptor\\PDB_MODELS\\peptide_chain\\reply_log',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'C:\\Users\\wiason\\Desktop\\try_combining2.pdb',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'C:\\Users\\wiason\\Desktop\\try_combining.pdb'],<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'main chimera import dialog': [u'E:\\A.Model_receptor\\model_env\\calc_receptor_rmsds.cmd',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'E:\\A.Model_receptor\\PDB_MODELS\\peptide_chain\\extract_peptide_from_PDB.cmd',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'E:\\A.Model_receptor\\PDB_MODELS\\3D39.pdb',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'E:\\A.Model_receptor\\PDB_MODELS\\3D39.fasta',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'E:\\A.Model_receptor\\PDB_MODELS\\3DTX.pdb',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'E:\\A.Model_receptor\\PDB_MODELS\\3B3I.pdb',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'E:\\A.Model_receptor\\PDB_MODELS\\2JCC.pdb',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'E:\\A.Model_receptor\\PDB_MODELS\\2J8U.pdb',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'E:\\A.Model_receptor\\PDB_MODELS\\1LP9.pdb',<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
u'E:\\A.Model_receptor\\PDB_MODELS\\1B0G.pdb']},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'>
'lastFilter': {'main chimera import dialog': 'all (guess type)'}},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'> 'update
check': {'last time': (2010, 3, 3, 12, 50, 48, 371000, None)},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'> 'version
tracking': {'last version': '1.4_b29093'},<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'> 'write
PDB dialog': {'multiSavePDB': 'single'}}<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=black face="Courier New"><span
lang=EN-US style='font-size:11.0pt;font-family:"Courier New";color:black'><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'><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 lang=EN-GB
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 class=MsoNormal align=center style='text-align:center'><font size=3
color=black face="Times New Roman"><span lang=EN-US style='font-size:12.0pt;
color:black'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<div>
<p class=MsoNormal><b><font size=2 color=black face=Tahoma><span lang=EN-US
style='font-size:10.0pt;font-family:Tahoma;color:black;font-weight:bold'>From:</span></font></b><span
class=apple-converted-space><font size=2 color=black face=Tahoma><span
lang=EN-US style='font-size:10.0pt;font-family:Tahoma;color:black'> </span></font></span><font
size=2 color=black face=Tahoma><span lang=EN-US style='font-size:10.0pt;
font-family:Tahoma;color:black'>Eric Pettersen [<a
href="mailto:pett@cgl.ucsf.edu">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">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><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;color:black'><u1:p> </u1:p></span><o:p></o:p></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'>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.<u1:p></u1:p><o:p></o:p></span></font></p>
</div>
<div>
<div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'><u1:p> </u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'>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.<u1:p></u1:p><o:p></o:p></span></font></p>
</div>
<div>
<div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'><u1:p> </u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'>--Eric <u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'><u1:p> </u1:p><o:p></o:p></span></font></p>
</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>
<p class=MsoNormal><font size=3 color=black face=Helvetica><span
style='font-size:12.0pt;font-family:Helvetica;color:black'>
Eric
Pettersen<u1:p></u1:p></span></font><font color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
</div>
<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<u1:p></u1:p></span></font><font color=black><span
style='color:black'><o:p></o:p></span></font></p>
</div>
</div>
<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><u1:p></u1:p></span></font><font
color=black><span style='color:black'><o:p></o:p></span></font></p>
</div>
</div>
<div>
<p class=MsoNormal><font size=3 color=black face=Helvetica><span
style='font-size:12.0pt;font-family:Helvetica;color:black'><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>
<div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'>On Mar 8, 2010, at 7:32 PM, Sumitro
Harjanto wrote:<u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt;color:black'><u1:p> </u1:p><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'><u2: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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Eric,<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u2:p> </u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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. =]<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> <u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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.<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u2:p> </u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks,<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Sumitro<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u2:p> </u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>-----------------------------------------------------------------------------------------------------<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u2:p> </u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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'><u2:p></u2:p><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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.<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u2:p> </u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>--------------------------------------------------------------------------------------------------<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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):<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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><u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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)<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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)<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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)<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u2:p> </u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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()<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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)<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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)<u2:p></u2:p></span></font><font color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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()<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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__<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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)<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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__<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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)<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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()<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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()<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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)))<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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__<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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)<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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__<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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)<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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"<u2:p></u2:p></span></font><font color=black><span
style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<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<u2:p></u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u2:p> </u2:p></span></font><font
color=black><span style='color:black'><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt;color:black'></u2:smarttagtype></span></span><u1:p> </u1:p><o:p></o:p></span></font></p>
</div>
</div>
</div>
</div>
</div>
</span>
<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>
</body>
</html>