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choderalab / ensembler

Automated omics-scale protein modeling and simulation setup.
http://ensembler.readthedocs.io/
GNU General Public License v2.0
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Fix MD5 issue in Travis. #88

Closed nhstanley closed 7 years ago

nhstanley commented 7 years ago

Changing from http to https fixes the error (though there are other, unrelated errors in the build now).

jchodera commented 7 years ago

Thanks! There's still lots of other things I unfortunately need to fix here before we can resurrect the master branch, but this helps!

nhstanley commented 7 years ago

I'll try to help where I can. I'd like to help get a python 3 version going as well, unless there's some unresolvable conflict with Modeller or some other package (too common).

jchodera commented 7 years ago

I think it should be possible! I've made some progress on that, and will try to do more over the Thanksgiving holiday.

There is a science issue right now we have to resolve as well: we've identified instances in which chirality of alpha carbons or peptide bonds are flipped during the MODELLER stage. We're trying to code up some tests for this using MDTraj (and hopefully submit those as MDTraj utilities) so we can protect against this:

https://github.com/choderalab/msm-pipeline/blob/utils/msmpipeline/utils.py

This is based on a tool for VMD that detects and fixes chirality errors.