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
ways:
- 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
restraints
- 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
appear.
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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