Retrieving the aligned (superposed) PDBs

[jeversbioprodict]

So Foldmason aligns the structures and in the HTML you can download the aligned PDBs. However, I think it would be great to get them using only the command line.

Also, the downloaded PDBs from the HTML are not (always?) aligned.
(The attached file is an HTML, but I had to add json to be able to upload it)
result_it20_go20_ge1_1XO0A_3NKHA.html.json

[gamcil]

There was a bug with transforming atomic coordinates for the PDB download which should be fixed in the current webserver, but the version distributed with the command line version is lagging behind a bit. If you get the underlying JSON data file (download from your HTML file, or run easy-msa with --report-mode 2/the msa2lddtjson module) and then upload it to the webserver with the "upload previous result" button it should be fine there. We should add this functionality directly to the command line version too.