In Selection Interface, I'm unable to customize the behavior of ActionMutate in the Mutation menu:

1. Select a residue, press 'M' for Mutation menu.

2. Manually check boxes for ResidueTypes I want to allow.

3. Click on background or 'B' to go back, or 'Y' to start Mutate.

4. Checkboxes reset (!) and Mutate follows default behavior.

Note: Within the Mutation menu, the buttons 'J', 'Z', and 'X' function as expected and effectively toggle "Apolar," "Polar," and "All" ResidueTypes; this successfully changes the behavior of ActionMutate. It seems that only manual adjustments are not registered.

TaskOperation elements in a RosettaScripts XML can be used to control the behavior of the packer at each residue, but it can be difficult to write these TaskOperation elements to produce desired behavior. Some TaskOperations behave non-intuitively, and it can be tough to follow the logic of ResidueSelectors.

It would be great if there were a button in the standalone to "Check TaskOperations," that could parse each TaskOperation in a RosettaScripts XML, and color which residues are designable (and to which residue types), which are restricted to repacking, and which cannot be repacked.

Allow users to load their favorite RosettaScripts into a local "cookbook," so they don't have to navigate the file system to access frequently-used RosettaScripts. Potentially, use this to distribute a handful of common or template RosettaScripts with the standalone.

Many people use the GREMLIN server for predicted contacts, which are output in a tabular format with a header line (example: http://openseq.org/sub_txt.php?id=1476807290).

Foldit can *almost* load this file, but requires two small revisions in the header line: You have to prefix the line with '##' and change the column name 'prob' to 'weight'. Is it possible to add support for parsing the raw GREMLIN output?

Foldit requires that you use the C-term VRT residue as the anchor residue in symmetry. Right now, this requires manually editing a .sym file every time you load a symmetric pose of a different size. If Foldit could just set the anchor residue automatically, behind the scenes, then users could use the symmetry definition files straight out of the Rosetta database.

Big inconvenience for anyone who wants to use the standalone more than once. Sometimes manifests as a "number of residues" mismatch, or "missing params file" error. Usually just crashes.

In sessions created from a FASTA file, the "Save Session" button appears to write an .ir_session file, but FolditStandalone later crashes when trying to load this session.

If you start a session with a FASTA file instead of a PDB, the session does not allow design, residue insertions, etc.

XML formatting errors are extremely common when editing RosettaScripts—especially among the non-programmers who are most likely to use the standalone. It would be great if we could catch some of the more common parsing exceptions (e.g. mismatched tags, tag does not exist), instead of crashing.