You know what they say about never releasing on a Friday… what does it say about me that I’m releasing on the last Friday before Christmas? 😬 Anyway, ISOLDE builds for ChimeraX 1.9 are now up. Enjoy! - ThreadSky

crolltristan.bsky.social • 184 days ago

You know what they say about never releasing on a Friday… what does it say about me that I’m releasing on the last Friday before Christmas? 😬

Anyway, ISOLDE builds for ChimeraX 1.9 are now up. Enjoy!

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crolltristan.bsky.social•184 days ago

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.

crolltristan.bsky.social•184 days ago

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.

crolltristan.bsky.social•184 days ago

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.

alexisrohou.bsky.social•183 days ago

Do you ever use the SMILES flavor of the command? I don’t, because I then don’t have a reliable way to generate a cif parametrization file for phenix polishing when I’m done in ISOLDE. (and also the SMILES gets sent to a server IIRC)

crolltristan.bsky.social•183 days ago

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?”).

crolltristan.bsky.social•183 days ago

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.

lucas.farnunglab.com•184 days ago

Anything major planned for the future?

crolltristan.bsky.social•184 days ago

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.

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