Ha! Well… at least it got there in the end.

Sadly not… iirc there was one that achieved brief infamy a year or two back which had a negative overall Q-score.

Oh, my poor baby. What have they done with you??

Mashing Pumpkins

Oooh, I know lots of those!

“What is biology?”

This brings back memories… climbing at Mt Arapiles, near the top-out about 30m off the ground I came across a crack very like this, with an odd white spot deep inside. Got closer to look, and realised it was a teeny tiny pair of fangs… unforgettable moment.

I’m guessing your problem is the dependency on the “sanity” package. Unfortunately that stopped being maintained a while back, and won’t install in the latest Python version.

🎶 When a muppet with teef finds a home on the reef, that’s a moray 🎵

(this is actually the old laptop I used for most of my original work on ISOLDE. Poor little thing… will try to look after it better in future)

Lady Cassandra??

Could of course fire up a “proper” docking package for that, but often this way seems quicker and easier (and helps get a better feel for the site, to boot). Take out the map, “isolde restrain distances” to maintain local conformation, then just play with it.

Both true. :) Although if it’s a novel ligand (or just something not in the CCD) the first point isn’t such a big issue. I don’t use it *that* often, but I do occasionally use it quickly assess hypotheses (“I wonder if{ligand} might plausibly fit this pocket?”).

Still trying to work that out, I’m afraid. While we have some interesting “ISOLDE-adjacent” stuff in the works, my day job currently doesn’t leave a lot of (well… any, really) time free for development of ISOLDE itself. Exploring options to support it in a more sustainable way.

One nice quality-of-life addition: all “open” commands now have an optional “cofr” argument. So for example…

open ligand.mol2 center cofr

or

open {smiles string} from smiles center cofr

… will put the ligand on ISOLDE’s crosshairs ready to move around and merge in.

While I haven’t had a chance to add anything really substantial to ISOLDE, the @www.cgl.ucsf.edu team have added a bunch of great new stuff to ChimeraX itself.

For people who managed to install older versions of ISOLDE into ChimeraX and found they promptly failed… sorry, that’s my fault. I didn’t RTFM about Python’s ‘~=‘ specifier. Thought “~=1.8.rc0” meant “>=1.8.rc0”, ==1.8.* when it actually means “>=1.8.rc0, ==1.*”.

🙃

Anyway, update to fix.