Re: [Chimera-users] Scripting to write / save multiple models into single pdb file

12 Mar 2010

      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) 

I found this codet on the chimera mailing list:

def save_reply_log(path):

   from chimera import dialogs

   r = dialogs.find('reply')

   text = r.text.get('1.0', 'end')

   f = open(path, 'w')

   f.write(text)

   f.close()

save_reply_log("/tmp/tmplog.txt")

but how do I incorporate this into my .cmd..? or must I now script in
python..?

thanks!

Cheers,

Sumitr.

________________________________

From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] 
Sent: 12 March 2010 6:24 AM
To: Sumitro Harjanto
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Scripting to write / save multiple models
into single pdf file

Hi Sumitro,

            Don't include "open" on the Unix command line.  You only
need that when typing into Chimera's own command line.

--Eric

On Mar 10, 2010, at 10:28 AM, Sumitro Harjanto wrote:

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@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@cgl.ucsf.edu] 
Sent: 10 March 2010 3:17 AM
To: Sumitro Harjanto
Cc: chimera-users@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