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.
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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)
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?”).
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.
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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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.