Daniel Parton

Thanks @gingerbeardman - interesting this is such a long-standing issue. I guess we'll have to hope that commonmark will eventually settle on a solution. Otherwise perhaps this could be implemented...

But the article is not actually published yet is it? On Mon, Apr 4, 2016 at 8:33 PM, John Chodera [email protected] wrote: > It was accepted, so we should let...

I don't think I have any control over it through their website, but you could contact Dryad and ask if they can make the data available now the proofs have...

It's Dryad's policy, not ours - I'm not sure why they have that policy. Maybe they think most researchers don't want to make their data available until the paper is...

Hi Mihir, Do you mean you only want to run the modeling stage of Ensembler, not the MD refinement steps? If so, you should use the main pipeline functions up...

So instead of using `quickmodel` you will want to use the main pipeline functions as described here: http://ensembler.readthedocs.org/en/latest/examples.html#example-using-the-main-pipeline-functions These are a set of functions which are to be performed in...

Hi, if you're not using Rosetta loopmodel, then you should just skip the `loopmodel` command. Modeller will be used when the `build_models` command is run. But the `align` command should...

Yes, that should be the top-level directory. Let me know if you still get errors.

Hi, so the way I wrote that error message is kind of wrong. It actually means that the directory `structures`, which should have been created when `ensembler init` was run,...

Yep, definitely use accession numbers if you need to use persistent IDs. The `--query` argument is passed directly to the UniProt search API, which allows you to search by accession...