Hi,
I have installed Modeller 9.13 (downloaded http://salilab.org/modeller/9.13/modeller-9.13.tar.gz and executed the Install file). Next, I created a shared library for a user defined constraint as follows:
gcc -shared -Wall -fPIC .../bin/modeller9.13/bin/mod9.13 --cflags --libs` `pkg-config --cflags glib-2.0` -I/usr/include/pythonXXX my_rsr.c my_rsr_wrap.c -o _my_rsr.so -lm
where XXX stands for different python versions I tried (e.g. 2.5,2.6,2.7)
When executing my python script via:
...bin/modeller9.13/bin/mod9.13 my_script.py or ...bin/modeller9.13/bin/modpy.sh pythonXXX my_script.py
I always get the error:
ImportError: .../bin/modeller9.13/modlib/modeller/_my_rsr.so: undefined symbol: Py_InitModule4_64
I tried to set the python path, but it didn't help.
How can I fix this?
On 2/9/15 4:07 AM, meier@lmb.uni-muenchen.de wrote: > ImportError: .../bin/modeller9.13/modlib/modeller/_my_rsr.so: undefined > symbol: Py_InitModule4_64
This means that you compiled the extension against a different Python version than the one you're trying to run it with. (If you use the mod9.13 script, it uses a built-in version of Python 2.3, so that's definitely not going to work unless you have a copy of the 2.3 headers on your system.)
Setting PYTHONPATH will probably just confuse things, since the modpy script does that already.
Ben Webb, Modeller Caretaker
Hello,
I'm working on a project that studies the effects of the alignments on the quality of the 3D models produced by modeller. basically I'll be using heuristics to iterativevly refine the alignment and hence result in a better 3D model by Modeller. My question is what's the simplest alignment method used by modeller that can produce me alignments between a target and a single template? and how would I see this alignment? how would I access it? for example there is this method: automodel.auto_align(). is this the simplest alignment producing function or there are other ways to produce weaker alignments? and how would I get a hold of this alignment produced by the function (in this case automodel.auto_align())?
Thank you.
________________________________________ From: modeller_usage-bounces@salilab.org modeller_usage-bounces@salilab.org on behalf of Modeller Caretaker modeller-care@salilab.org Sent: Monday, February 9, 2015 5:43 PM To: meier@lmb.uni-muenchen.de; modeller_usage@salilab.org Subject: Re: [modeller_usage] error: Py_InitModule4_64
On 2/9/15 4:07 AM, meier@lmb.uni-muenchen.de wrote: > ImportError: .../bin/modeller9.13/modlib/modeller/_my_rsr.so: undefined > symbol: Py_InitModule4_64
This means that you compiled the extension against a different Python version than the one you're trying to run it with. (If you use the mod9.13 script, it uses a built-in version of Python 2.3, so that's definitely not going to work unless you have a copy of the 2.3 headers on your system.)
Setting PYTHONPATH will probably just confuse things, since the modpy script does that already.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage _______________________________________________ modeller_usage mailing list modeller_usage@salilab.org https://salilab.org/mailman/listinfo/modeller_usage
On 02/09/2015 09:36 AM, Mouses Stamboulian wrote: > I'm working on a project that studies the effects of the alignments > on the quality of the 3D models produced by modeller. basically I'll > be using heuristics to iterativevly refine the alignment and hence > result in a better 3D model by Modeller. My question is what's the > simplest alignment method used by modeller that can produce me > alignments between a target and a single template? and how would I > see this alignment? how would I access it? for example there is this > method: automodel.auto_align(). is this the simplest alignment > producing function or there are other ways to produce weaker > alignments? and how would I get a hold of this alignment produced by > the function (in this case automodel.auto_align())?
The simplest alignment is alignment.align(): http://salilab.org/modeller/9.14/manual/node306.html
The simplest way to use it would be to modify the example at that URL for your inputs, and use it to generate the .ali file that you then feed to automodel.
Ben Webb, Modeller Caretaker
Thank you. Ill give that a go.
Sent from my iPhone
> On Feb 10, 2015, at 10:53 PM, Modeller Caretaker modeller-care@salilab.org wrote: > >> On 02/09/2015 09:36 AM, Mouses Stamboulian wrote: >> I'm working on a project that studies the effects of the alignments >> on the quality of the 3D models produced by modeller. basically I'll >> be using heuristics to iterativevly refine the alignment and hence >> result in a better 3D model by Modeller. My question is what's the >> simplest alignment method used by modeller that can produce me >> alignments between a target and a single template? and how would I >> see this alignment? how would I access it? for example there is this >> method: automodel.auto_align(). is this the simplest alignment >> producing function or there are other ways to produce weaker >> alignments? and how would I get a hold of this alignment produced by >> the function (in this case automodel.auto_align())? > > The simplest alignment is alignment.align(): > http://salilab.org/modeller/9.14/manual/node306.html > > The simplest way to use it would be to modify the example at that URL for your inputs, and use it to generate the .ali file that you then feed to automodel. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
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meier＠lmb.uni-muenchen.de -
Modeller Caretaker -
Mouses Stamboulian