"similarstructures ligands" does not check if user wants to fetch that many structures

[Elaine Meng]

I figured it was just an oversight since "similarstructures cluster" and "similarstructures traces" will ask the user to make sure if opening a bunch of structures is OK, but "similarstructures ligands" does not. When testing something with several hundred hits I had to force quit when it started doing all the fetches!

Tested in UCSF ChimeraX version: 1.9.dev202411010646 (2024-11-01)

[Elaine Meng]

Actually what I was really going to test in the first place is whether you even need a similarstructures fetchcoords command any more, since these other commands will initiate it as needed. Are there plans to remove it? Or am I missing something, is there a reason to have it separately? Thanks

[Tom Goddard]

Fixed.

The Ligands button on the similar structure GUI was asking whether to download the structures but the equivalent command was not asking. I made the command ask. On a fast network connection (1 Gbit) the download of a few hundred structures took a few minutes, so not too long, and the alignment if the structures are already fetched and cached takes about 15 seconds for 200 structures.

The fetchcoords command is rarely needed. As you note the traces and clustering already fetch the coordinates automatically. I consider this a utility command. It adds the C-alpha coordinates to the .sms file so that future traces/clustering operations are fast. Because it can take a long time to fetch the structures on a slow network connection, the fetchcoords command can be run to separate this step. In the future I might improve it to allow doing all the fetching in the background so you can continue to use ChimeraX. At any rate, I plan to keep the fetchcoords command, although it is seldom needed.