[Chimera-users] Scripting to write / save multiple models into single pdf file
Sumitro Harjanto
u0601918 at nus.edu.sg
Wed Mar 10 10:28:06 PST 2010
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.
So I advanced a little and try to run a .cmd file using the command
prompt:
>chimera --nogui open
e:\A.Model_receptor\model_env\calc_receptor_rmsds.cmd
But again I got the same error message:
***********************************************************************
Chimera failed abnormally; the exit code was: 1
Use -debug command line option for the full error message.
************************************************************************
Below is what I see after adding "--debug" to the command:
***********************************************************************
Cannot execute 'gzip': no automatic decompression of .Z files
Traceback (most recent call last):
File "E:\Chimera\share\chimeraInit.py", line 425, in init
Chimera.openModels.open<a, prefixableType=1>
File "E:\Chimera\share\chimera\__init__.py", line 1405, in open
Raise ValueError, "Unknown model type"
ValueError: Unknown model type
Error while processing open:
ValueError: Unknown model type
File "E:\Chimera\share\chimera\__init__.py", line 1405, in open
Raise ValueError, "Unknown model type"
See reply log for Phyton traceback.
Opening 2HN7.pdb...
1 model opened
Opened ... ... ... (and actually continues to complete my script)
***********************************************************************
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.
Any way to go around this..? I don't know if it helps, but below is my
"preferences" file
*********************************************************************
{'Model Panel': {'freqButs': {'2D Diagram': False,
'activate': False,
'activate all': True,
'activate only': True,
'add hydrogens...': False,
'add/edit note...': True,
'attributes...': True,
'blast protein...': True,
'clipping...': True,
'close': True,
'color by SS...': False,
'compute SS': True,
'copy/combine...': True,
'deactivate': False,
'focus': True,
'hide': False,
'match...': True,
'minimize...': False,
'rainbow...': True,
'rename...': True,
'render/sel by attr...': True,
'select': True,
'select chain(s)...': True,
'sequence...': True,
'show': False,
'show all atoms': True,
'show only': True,
'surface main': True,
'tile...': True,
'toggle active': True,
'trace backbones': True,
'trace chains': True,
'transform as...': True,
'write PDB': True},
'lastUse': 1268231127.7550001},
'Nucleotides': {'slab styles': {}},
'Ribbon Styles': {'atoms': {}, 'scaling': {}, 'xsections': {}},
'Tools': {'autoStart': {},
'confirmOnStart': {},
'dirList': [],
'inFavorites': {'Command Line': 2,
'Model Panel': 0,
'Reply Log': 4,
'Sequence': 3,
'Side View': 1},
'onToolbar': {}},
'command line gui': {'remembered commands': ['select #0:2-182.A at C',
'write selected format pdb
0 E:\\A.Model_receptor\\PDB_MODELS\\1W72_c.pdb']},
'initial size': {'Window size': (525, 513)},
'miller browser': {'dirHistory':
[u'E:\\A.Model_receptor\\Chimera_log_parser',
'C:\\Users\\wiason\\Desktop'],
'fileHistory': {'':
[u'E:\\A.Model_receptor\\Chimera_log_parser\\RMSD_raw.txt',
u'E:\\A.Model_receptor\\PDB_MODELS\\peptide_chain\\reply_log',
u'C:\\Users\\wiason\\Desktop\\try_combining2.pdb',
u'C:\\Users\\wiason\\Desktop\\try_combining.pdb'],
'main chimera import dialog':
[u'E:\\A.Model_receptor\\model_env\\calc_receptor_rmsds.cmd',
u'E:\\A.Model_receptor\\PDB_MODELS\\peptide_chain\\extract_peptide_from_
PDB.cmd',
u'E:\\A.Model_receptor\\PDB_MODELS\\3D39.pdb',
u'E:\\A.Model_receptor\\PDB_MODELS\\3D39.fasta',
u'E:\\A.Model_receptor\\PDB_MODELS\\3DTX.pdb',
u'E:\\A.Model_receptor\\PDB_MODELS\\3B3I.pdb',
u'E:\\A.Model_receptor\\PDB_MODELS\\2JCC.pdb',
u'E:\\A.Model_receptor\\PDB_MODELS\\2J8U.pdb',
u'E:\\A.Model_receptor\\PDB_MODELS\\1LP9.pdb',
u'E:\\A.Model_receptor\\PDB_MODELS\\1B0G.pdb']},
'lastFilter': {'main chimera import dialog': 'all
(guess type)'}},
'update check': {'last time': (2010, 3, 3, 12, 50, 48, 371000, None)},
'version tracking': {'last version': '1.4_b29093'},
'write PDB dialog': {'multiSavePDB': 'single'}}
************************************************************************
****************************
________________________________
From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
Sent: 10 March 2010 3:17 AM
To: Sumitro Harjanto
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Scripting to write / save multiple models
into single pdf file
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.
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
that 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.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
On Mar 8, 2010, at 7:32 PM, Sumitro Harjanto wrote:
Hi Eric,
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. =]
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.
Thanks,
Sumitro
------------------------------------------------------------------------
-----------------------------
Chimera failed abnormally; the exit code was: 1
Use -debug command line option for the full error message.
------------------------------------------------------------------------
--------------------------
Cannot execute 'gzip': no automatic decompression of .Z files
Traceback (most recent call last):
File "E:\Chimera\share\__main__.py", line 65, in <module>
value = chimeraInit.init(sys.argv)
File "E:\Chimera\share\chimeraInit.py", line 401, in init
extension.startup(startExtensions)
File "E:\Chimera\share\chimera\extension\base.py", line 1056, in
startup
manager.autostartTools(extNames)
File "E:\Chimera\share\chimera\extension\base.py", line 959, in
autostartTools
emo.activate()
File "E:\Chimera\share\ModelPanel\ChimeraExtension.py", line 23, in
activate
display(self.module('base').ModelPanel.name)
File "E:\Chimera\share\chimera\dialogs.py", line 77, in display
dialog = find(name, create=1)
File "E:\Chimera\share\chimera\dialogs.py", line 62, in find
return d()
File "E:\Chimera\share\chimera\baseDialog.py", line 523, in __init__
BaseDialog.__init__(self, master, *args, **kw)
File "E:\Chimera\share\chimera\baseDialog.py", line 244, in __init__
self.fillInUI(self.__top)
File "E:\Chimera\share\ModelPanel\base.py", line 217, in fillInUI
self._addColumns()
File "E:\Chimera\share\ModelPanel\base.py", line 436, in _addColumns
self._buildTable()
File "E:\Chimera\share\ModelPanel\base.py", line 454, in _buildTable
% len(filter(lambda s: s == 1, self.shownColumns)))
File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 1306, in __init__
cnf, kw)
File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 307, in __init__
self.tk.call(widgetName, self._w, *extra)
_tkinter.TclError: invalid command name "tixScrolledHList"
Return code: 1
Press return or enter to to exit
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