kortemme-lab / pull_into_place Goto Github PK

Mac mouses don't always have a right-click button, and it seems that the operating system doesn't automatically translate Ctrl-click to right-click. So I should add that feature.

Just to give users peace of mind, I think the 04 and 06 scripts (i.e. picking models/designs to carry forward) should log whether or not they're preferring high or low values for each metric. This information ultimately comes from the names of the filters, but that's pretty indirect, so I think it'd be good to let the user know what's happening.

I don't really think there's anything I can do about this, but it is confusing. I should put a big note in the documentation to point out that you may need to try making the window bigger.

Hello. I want to use your guide on Read the Book site. There are any changes in PIP since 2016? If I'll go scenario, don't I meet any troubles because of upgrades?
I saw that some scripts uses your cluster. How can I do that tutorial on my local machine? It's possible, to copy modules, that your script require?

Now that most of the config files aren't stored in the root directory, we can't hard-code paths to the included XML files: shared_defs.xml and filters.xml. Unfortunately, we also can't use %% substitution for these files either: it seems that the xml includes are processed before the substitutions are. This fact makes this issue a lot harder to resolve.

My first idea is just to put these paths in the root directory. The easiest way to do this would be to change the workspace functions so the just return a path relative to the root, rather than calling find_path(). The install script would also have to change. There'd need to be a step after all the others that calls find_path() on the two paths in question, then makes a symlink into the root directory for each one.

Another possibility is to roll our own substitution. I've thought before about using Jinja, just for the more expressive power it offers, but it'd mean managing some temporary files and adding a possibly tough dependency. The file management would be pretty easy, I could just put the generated file in the focus dir. The dependency isn't so bad, either. It'd just be Jinja2 and MarkupSafe. This may be something to think about.

Of course, the answer of the future is to use pyrosetta. But that remains too much work, for the moment.

The XSD XRW changed how rosetta scripts are parsed. Scripts are now required to be valid XML files, which allows the parser the do better validation and error-reporting.

Namely the loophash_db and the vall file. For now we're just copying these files from Xingjie, but PIP will need to generate them itself if we want this protocol to be useful after we've left the lab.

This is a really nice feature, but nobody knows about it because the demo doesn't mention it. I'll need to find/make a *.sho file for KSI and add it to the ksi_inputs directory.

This is due to the way paths are concatenated. PIP does rsync_path + / + workspace_name. But if rsync_path is of the form user@hostname:, the path ends up in root rather than the user's home directory.