[cctbxbb] indexing success rates
asbrewster at lbl.gov
Sat Feb 3 00:37:10 PST 2018
Hi James, thanks. I looked at random image 15 and after trying a bunch of
stuff it indexes fine if I use indexing.method=fft3d. The default for
stills processing is fft1d, so I find this super interesting.
For what it's worth, I pretty much never process stills without a target
cell. I generated ~30 random images using your script and indexed them,
then I got the unit cells with "dials.show *refined*.json | grep cell".
They were all about the same. So I re-indexed random image 15 using fft1d
but I also specified known_symmetry.cell=50,60,70,90,90,90 and it indexed
So, either indexing.method=fft3d or known_symmetry.cell=50,60,70,90,90,90
is sufficient to index random image 15. Certainly for experimental data I
would recommend using known_symmetry as the results are always better.
However, I'd like to look deeper at fft1d vs fft3d at some point.
On Fri, Feb 2, 2018 at 1:35 PM, James Holton <jmholton at lbl.gov> wrote:
> While testing the new simTBX diffraction image simulator Aaron and I found
> that some rather beautiful-looking images still won't index. Subsequently,
> I followed up with mosflm, which does succeed in these cases, even without
> prior knowledge of the cell or space group.
> I have now run this 1000 times, varying only the crystal orientation, and
> found 171 cases of dials.stills_process failing to index the simulated
> image whereas mosflm had no trouble, and 5 cases where mosflm failed and
> dials.stills_process succeeded. There were no overlapping cases where both
> programs failed.
> I have tarballed up the relevant files here:
> The tarball contains a "runme.com" shell script for reproducing these
> results, and also the tst_nanoBragg_forindex.py jiffy for making a test
> image given a provided random-number seed. For example:
> libtbx.python ./tst_nanoBragg_forindex.py random 15
> will create a file called noiseimage_001.cbf that dials.stills_process
> cannot index (at least in my hands). For those of you who don't have
> mosflm installed, the tarball incluses a copy, and the "autoindex.com"
> script should run on any linux system.
> Any ideas as to why there is this discrepancy? Feels like an opportunity
> for a non-trivial improvement.
> Something to ponder over the weekend, I suppose. Note that I recently
> checked in a few bug fixes to simTBX, but this analysis is unaffected by
> them, so you shouldn't have to update your build to reproduce this.
> -James Holton
> MAD Scientist
> cctbxbb mailing list
> cctbxbb at phenix-online.org
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