[cctbxbb] [Dials-support] indexing success rates

Aaron Brewster asbrewster at lbl.gov
Sat Feb 3 01:11:04 PST 2018

Right, typically if I don't know the cell, I'll index a bunch of images
with no target, then use cluster.unit_cell on the results to get a
consensus cell, then re-index with that cell.

For dials.stills_process, the default of fft1d works pretty well generally,
but to get the best results, indexing.method_list=fft1d,fft3d might be
better.  There, if the first method fails the second is tried.
real_space_grid_search can also be used.

Getting a specific image in a composite file (such as hdf5) isn't a use
case I've hit often, so I don't have an easy solution there.  It's possible
an image range parameter to dials.import would be useful?


On Sat, Feb 3, 2018 at 1:02 AM, Graeme Winter <graeme.winter at gmail.com>

> Hi Aaron
> (and DIALS)
> For stills / single images - should dials.index switch by magic to default
> fft1d?
> Of is that the responsibility of e.g. xia2 / cctbx.xfel to worry about?
> It has to be said, more often than not, particularly for screening, we do
> not know cell / symmetry a priori (at diamond anyways)
> A related question
> If I have a data block / strong pickle from 1000 stills, how can I index
> e.g. image 672? Do I have to split this into 1000 separate things?
> @JH - thanks for this - I think some rigorous testing will be useful here.
> Cheers Graeme
> On 3 Feb 2018, at 08:37, Aaron Brewster <asbrewster at lbl.gov> wrote:
> 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
> fine.
> 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.
> Cc'ing dials-support.
> Thanks!
> -Aaron
> 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:
>> http://bl831.als.lbl.gov/~jamesh/bugreports/dials_index_020218.tgz
>> 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.
>> Cheers,
>> -James Holton
>> MAD Scientist
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