Hello Ben,

I’ve rebuilt IMP from the git repo https://github.com/salilab/imp.githttp://github.com/salilab/imp.git after upgrading my Mac to El Capitan and now IMP throws an AttributeError:

$ ./setup_environment.sh python ../imp_tutorial/rnapolii/modeling/modeling.py Traceback (most recent call last): File "../imp_tutorial/rnapolii/modeling/modeling.py", line 78, in <module> m = IMP.Model() File "/opt/imp_latest/imp-fast/lib/IMP/__init__.py", line 4935, in __init__ self.this.append(this) AttributeError: 'Model' object has no attribute ‘this'

I’ve cleaned up my homebrew install and went step by step through the entire IMP installation process from scratch. The installation seems to have completed fine. This is my python virtual environment:

biopython==1.66 cycler==0.10.0 distribute==0.6.34 matplotlib==1.5.1 nose==1.3.7 numpy==1.11.0rc2 pyparsing==2.1.1 python-dateutil==2.5.1 pytz==2016.3 scikit-learn==0.17.1 scipy==0.17.0 six==1.10.0 wsgiref==0.1.2

I checked that I am sourcing the correct new IMP environment. I am running modeling.py from within the python virtual. So what am I missing?

thanks,

Isabelle

On Mar 20, 2015, at 4:51 PM, Ben Webb <ben@salilab.orgmailto:ben@salilab.org> wrote:

On 03/19/2015 05:56 PM, Isabelle Phan wrote: How do I install working examples for pmi rnapolii?

For the sake of completeness: the place to find longer worked applications of IMP like this is the tutorial: http://integrativemodeling.org/2.4.0/doc/tutorial/rnapolii_stalk.html

(You can also look at the actual modeling scripts we used for our papers, at http://integrativemodeling.org/systems/, but these don't tend to be as nicely commented and described ;)

The 'examples' directory in each IMP module is typically used to demonstrate the use of IMP functions and classes - there's rarely space or time in a short example to model a "real" system.

Ben -- ben@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle _______________________________________________ IMP-users mailing list IMP-users@salilab.org https://salilab.org/mailman/listinfo/imp-users

Thanks Ben, downgrading to swig 3.0.7 did it.

Isabelle

On Mar 24, 2016, at 8:09 PM, Ben Webb <ben@salilab.orgmailto:ben@salilab.org> wrote:

On 3/24/16 5:30 PM, Isabelle Phan wrote: I’ve rebuilt IMP from the git repo https://github.com/salilab/imp.githttp://github.com/salilab/imp.git after upgrading my Mac to El Capitan and now IMP throws an AttributeError:

$ ./setup_environment.sh python ../imp_tutorial/rnapolii/modeling/modeling.py Traceback (most recent call last): File "../imp_tutorial/rnapolii/modeling/modeling.py", line 78, in <module> m = IMP.Model() File "/opt/imp_latest/imp-fast/lib/IMP/__init__.py", line 4935, in __init__ self.this.append(this) AttributeError: 'Model' object has no attribute ‘this'

If you're using SWIG 3.0.8, then you're liking hitting this SWIG bug: https://github.com/swig/swig/issues/583

The simplest solution would be to use SWIG 3.0.7 instead.

Ben -- ben@salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle _______________________________________________ IMP-users mailing list IMP-users@salilab.org https://salilab.org/mailman/listinfo/imp-users