[chimerax-users] Clipper's strange behaviour

[Tristan Croll]

Summary after some investigation on my part:

The MTZ file in question was generated from a cryo-EM map using
phenix.map_to_structure_factors. Due to the large box size of cryo-EM maps,
such files tend to be *huge* - in this case, 1.8 billion reflections, about
800 times larger than the largest crystallographic dataset in the wwPDB.
That alone wouldn't necessarily be a problem, but as well as the map
amplitudes and phases (F/PHI), the MTZ output also contains a
(undocumented, as far as I'm aware) "F-obs/SIGF-obs" array - the data type
normally used to store crystallographic observations. Clipper interprets
this as such, and tries to generate a set of live-recalculating maps. This
is where things were going a bit awry: the extreme number of reflections
broke some (naive) assumptions I'd made in the outlier rejection step,
causing it to blow out from <1 second to almost 5 hours (!) - that's now
been fixed (will be in the next full or dev release, whichever comes
first), which should have the knock-on effect of making the loading of
large crystallographic datasets much faster. On my Windows laptop (32 GB
RAM, 32 GB swap) it manages to eventually generate the maps; on my Linux
desktop (32 GB RAM, 2 GB swap) it eventually gets killed when it runs out
of memory. The upshot right now:

- unless you have a very good reason to do otherwise, just work directly
with the cryo-EM map rather than converting to structure factors first.
- if you do need to be working with structure factors, you can use the
Reflection File Editor in the Phenix GUI to copy just the F/PHI column to a
new MTZ. That opens in about 2-3 minutes and behaves as expected.

I'll also look into adding a GUI option to choose which columns to actually
turn into maps when a multi-dataset MTZ file is opened.

-- Tristan

On Fri, Jan 13, 2023 at 8:22 AM André Graça via ChimeraX-users <
chimerax-users at cgl.ucsf.edu> wrote:

> Hi everyone!
>
>
>
> Is there any known issue with Clipper plugin for ChimeraX?
>
> After installing clipper and restarting ChimeraX, the software is not
> responding after I execute the Open command.
>
> I expect that it takes some time to open an .mtz file as the map needs to
> be calculated, however I have waited more than 45 minutes and ChimeraX
> keeps unresponsive…
>
>
>
> I am using Chimera 1.5 and I installed the (hopefully compatible) version
> of Clipper 0.19.0
>
>
>
> Did anyone faced the same problem? Let me know if you have a fix or trick
> ;)
>
>
>
> Thanks for any feedback in advance,
>
> André
>
>
>
>
>
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>
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