[phenixbb] ISOLDE 1.0b4 released

Tristan Croll tic20 at cam.ac.uk
Fri Jan 3 02:28:30 PST 2020

Happy new year to all my colleagues in the structural biology community! 
I'm delighted to announce the release of ISOLDE 1.0b4 to coincide with 
the stable release of ChimeraX 0.91.

What is ISOLDE?

ISOLDE is a plugin to UCSF ChimeraX, designed to ease the task of 
macromolecular model building into low-to-medium resolution maps derived 
from crystallographic or electron cryo-microscopy (cryoEM) experiments. 
Historically, this has been an extremely challenging task, since at low 
resolutions the maps alone are insufficient to precisely place 
individual atoms. ISOLDE aims to reduce this challenge in a number of 

- Rebuilding is accomplished via GPU-accelerated interactive molecular 
dynamics (using OpenMM and the AMBER molecular dynamics forcefield) to 
make the task feel as close as possible to what it might be like to work 
with a real physical molecule.
- Geometric validation of protein backbone and sidechain conformations 
is performed in real time, allowing you to see problem sites directly on 
the model as you work with it.
- Remodelling can be performed by directly tugging on atoms, or via the 
interactive addition and removal of position, torsion and/or distance 
- For crystallographic datasets, structure factors are constantly 
recalculated in the background as the model coordinates change - as the 
model improves, you see the map improve.

For more details, see https://isolde.cimr.cam.ac.uk/.

To install it for Linux, MacOS or Windows 10, go to 
http://preview.cgl.ucsf.edu/chimerax/download.html#release and install 
the **0.91** release build for your operating system.

(IMPORTANT NOTES: this build of ISOLDE will **only** work with version 
0.91 of ChimeraX. Additionally, Ubuntu users should use the "Generic 
Linux" ChimeraX build - the Ubuntu builds use compilers that are not 
compatible with ISOLDE).

Start ChimeraX, go to Tools/More Tools... and follow the links to 
install ISOLDE. Equivalently, just type "toolshed install isolde" on the 
ChimeraX command line. You can then start ISOLDE via 
Tools/General/ISOLDE or the command "isolde start". If this is your 
first time using it I highly recommend running either or both of the 
first two tutorials found in the top left of the ISOLDE panel that will 

A short list of what's new since 1.0b3:

- source code for ISOLDE and its "sister" package ChimeraX-Clipper are 
now on GitHub at https://github.com/tristanic/isolde and 
https://github.com/tristanic/chimerax-clipper respectively.
- integration with ChimeraX session save/restore framework. "save 
session.cxs" will save a snapshot of all models, maps and strucuture 
factors including all current ISOLDE restraints, and "load session.cxs" 
will return you to where you left off.
- added new adaptive torsion restraint implementation (a periodic 
analogue to Geman-McClure distance restraints) to restrain protein 
torsions to their current geometry or to a reference model. For details, 
type "usage isolde restrain torsions" on the ChimeraX command line and 
click the link in the log.
- documentation is now integrated with the ChimeraX documentation 
framework. In particular, "usage {command}" now provides a link to full 
documentation in the ChimeraX log window.
- improved behaviour (speed and stability) of energy minimiser
- significantly improved initial startup and simulation start times
- clearer indication of simulation state (running/paused)
- remote Python interface for communication with other packages
- various improvements and bug-fixes to handling of crystallographic 
data. In particular: better handling of anisotropic datasets, and 
improved stability of bulk solvent and scaling calculations.
- improved performance of live crystallographic map updates.
- support for multiple independent sets of adaptive distance restraints 
(currently only available via the Python API). For example, one set may 
be used to maintain internal geometry, while another represents 
crosslinking/mass spec or evolutionary coupling restraints.
- "Demo" button on ISOLDE GUI retired and replaced with a "Tutorials" 
drop-down menu.
- added tugging support in ChimeraX VR (thanks to Tom Goddard). ChimeraX 
currently supports VR only in Windows.

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