[phenixbb] ISOLDE 1.0b5 release

Tristan Croll tic20 at cam.ac.uk
Mon Apr 6 07:19:55 PDT 2020

Hi all,

For those still lucky enough to be working on molecular model building 
during this crisis, I've just pushed ISOLDE 1.0b5 out to the ChimeraX 
ToolShed (to work with the ChimeraX 0.93 release version - download from 
http://preview.cgl.ucsf.edu/chimerax/download.html#release, then install 
ISOLDE from within ChimeraX via Tools/More Tools...). While development 
has been a little light since version 1.0b4 due to travel in February 
and then, well... everything since, there are a few new features and 
bug-fixes worth downloading for:

- Perhaps the biggest improvement isn't actually mine - thanks to some 
stellar work by Tom Goddard at UCSF, ChimeraX's ribbon drawing is now 
ten times faster than before. Particularly for those working with very 
large models, this drastically reduces the lag time upon finishing an 
interactive simulation and returning to the default display mode.

- I've done some optimisations to the methods for choosing the initial 
map contour levels and the MDFF coupling constant (how strongly the map 
"pulls" on the model during simulations). They're now about 20 times 
faster, removing most of the delay on initial preparation of a model for 

- If you're lucky enough to be working on a multi-GPU machine, you can 
now explicitly specify the GPU to use for simulations with the command 
"isolde set gpuDeviceIndex {a number}" (you may need to experiment to 
work out which GPU is which)

- You can adjust the number of simulation steps between GUI updates with 
"isolde set timeStepsPerGuiUpdate". This is particularly useful for 
slower GPUs - your simulation won't actually run faster, but your 
experience of it will be much smoother. The default value of 50 works 
well for high-end GPUs; for (for example) light-weight MacBook GPUs a 
value of 10 may be more suitable. Performance curves for a few of the 
machines available to me can be found at 

- The command "clipper symmetry #{model number}" will draw a unit cell 
with all rotational symmetry and screw axes (mirror symmetry is not yet 
handled). The depiction is still a work in progress, but the 
fundamentals are there.

- While not new to 1.0b5, a reminder that since 1.0b4 ISOLDE is fully 
compatible with ChimeraX's session save/restore. The command "save 
{filename}.cxs" will save your current session (including your model(s), 
all custom restraints, maps, weightings and visualisation state) to a 
file which can be reopened on the same or another machine to pick up 
exactly where you left off.

Known bug: (seemingly only) on Linux machines, certain links to the help 
files (e.g. by typing "usage isolde" on the command line and then 
clicking the "isolde adjust distances"link in the log) sometimes cause 
segmentation faults if the help browser is not already open, crashing 
ChimeraX. This appears to be a bug in the Qt 5.12 web browser 
implementation, but so far has proven near-impossible to isolate. To 
avoid it, simply make sure the help browser is open (Help/User Guide) 
before clicking any links in the log.

I very much hope you find it useful.

Stay healthy!


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