ViewDockX should facilitate correct receptor vs. ligand classification from Maestro files

[Elaine Meng]

Suggestions are that ViewDockX should either:

(A) read the receptor/ligand attribute from Maestro files and exclude those marked as receptor from the ligand table. No change for other formats or if Maestro file doesn't include ligand/receptor attribute. This may be better than (B), since it won't bug people using other formats.

• OR -

(B) require specifying ligand models at startup: blank atomspec not allowed when starting from command, model chooser shown when started from Tools menu.

[Conrad Huang]

I'm somewhat reluctant to add heuristics for specific formats. If you use Maestro files, just "viewdock #1.2". Why punish people who use mol2?

[Elaine Meng]

Suggestion (A) specifically excludes only those marked “receptor" by Maestro, not affecting other formats.  Without this “heuristic” (which is hardly a heuristic, you’re not guessing what the receptor is, the file is telling you) I’ll bet you a million dollars that most people will just start the tool without specifying models, such as from the Tools menu, and then its behavior will be messed up.

[Conrad Huang]

So what do you do with other models which are marked as neither ligand nor receptor because they were not opened from Maestro files?

[Elaine Meng]

Same thing as whatever you are doing now (if anything) to tell if models are docking results.  If nothing, then nothing.  Only the Maestro “receptor” designation excludes the model from the list of docking results.

[Elaine Meng]

Fixed in Maestro tool version 1.3 as discussed in the comments for #2343.