ISOLDE: Bringing structural biology to life

ISOLDE

Frequently asked questions

What do I need to run it?

The short answer: ideally, a single modern workstation with the best GPU you can afford. However, ISOLDE is still usable even on a MacBook Air. ISOLDE is distributed for Windows, MacOS and Linux (built in CentOS 7 using devtoolset-3).

The longer answer: molecular dynamics (MD) is a computationally extremely demanding task. The MD engine underlying ISOLDE (OpenMM) relies heavily on GPU-accelerated computing to achieve usable speed in a workstation environment. The better your GPU, the better your experience in ISOLDE will be. Using the demo model bundled with ISOLDE (a 229-residue protein model with a 3 Angstrom resolution X-ray map) with live map recalculation turned off, my desktop Xeon workstation equipped with a Nvidia Titan Xp achieves just under 20 coordinate updates (1000 simulation steps) per second while maintaining a graphics framerate of 30-40 frames per second. My "power" laptop (a gaming model with an Intel Core i7 CPU and an Nvidia GTX1070 GPU) gives essentially indistinguishable performance for the same model. At the other end of the scale, my MacBook Air will run this model (and larger models running into the thousands of residues) - but only at a rate of 2-3 coordinate updates per second. Note, however, that you rarely need to simulate the whole model at once in ISOLDE - just a small buffer region around the site you wish to fix - so it is still very possible to do useful work on such a machine.

Oh - and you'll also want to be working with a real mouse. Trackpad support is a work in progress.

How do I get it?

ISOLDE is distributed as a plugin to UCSF ChimeraX, and can be easily installed via its built-in Tool Shed. See here.

(Important Note: ISOLDE 1.0 requires ChimeraX 1.0, and will not work with earlier versions)

Regular development builds are made available on the Tool Shed. These will be built to work with the latest daily builds of ChimeraX, and at this stage there is no guarantee of backward compatibility.

How do I use it?

ISOLDE comes bundled with comprehensive documentation of its GUI and (for the adventurous) its Python API. This is also provided .

 

 

I'm having installation or running issues. Help?

(legacy bug) In Linux, ChimeraX crashes when I load a model in ISOLDE

(Note: as of ChimeraX 0.93, all ChimeraX Linux builds use the same version of GCC, making the Ubuntu builds safe to use with ISOLDE. The below advice only applies to ChimeraX versions 0.92 or older.)

For Linux, ISOLDE is compiled against the RedHat rpm build of ChimeraX using gcc 4.9, to be as close as possible to a lowest common denominator for modern Linux operating systems. Unfortunately, the ChimeraX releases for Ubuntu are built with much newer GCC versions and are not compatible with ISOLDE. If you're using Ubuntu, you'll need to work with the "Generic Linux 64-bit" build of ChimeraX.

(legacy bug) I installed ChimeraX 0.9/ISOLDE 1.0b3 and get a ModuleNotFoundError when loading a model

In ChimeraX 0.9 there is a bug in the Tool Shed causing it to ignore the ChimeraX version requirement when installing a package as a dependency of another. This is causing the latest development build of Clipper (built for the ChimeraX 0.91 daily builds) to be installed. Due to API changes in ChimeraX this is not backward-compatible with ChimeraX 0.9. To correct the issue you have two options:

1. (Recommended) Download and install the latest ChimeraX daily build, and install ISOLDE into that. This will give you the latest ISOLDE and Clipper dev builds.

2. Downgrade Clipper to the correct version. Go to Tools/More Tools..., find and click the link for Clipper, click the "Release History" tab, then scroll down until you find the link to 0.9.4 for your operating system. Click the link to install, then restart ChimeraX when done.

ISOLDE is developed and maintained by Tristan Croll in the lab of Randy Read at the Cambridge Institute for Medical Research and supported by Prof. Read's Wellcome Trust Principal Research Fellowship 209407/Z/17/Z. Development and testing has been aided by the generous donation of a GTX Titan Xp GPU by NVIDIA Corporation.

Website design by Tristan Croll based on Hielo by Templated under a CC BY 3.0 license. Powered by Django-CMS.