Hi Keitaro, In Phenix, we set use_internal_variance to false whenever possible. We had users ask about the difference in merging statistics, which led to the discussion about the parameter with Richard. We picked the default that is mostly consistent with previous versions and added an option to change it, but we must have missed certain cases where the parameter was not set. Thanks for finding it! phenix.merging_statistics is just a different way for calling the same code as iotbx.merging_statistics, so the default value for use_internal_variance is true on the command-line. However, I explicitly set the default to false in the GUI for phenix.merging_statistics. phenix.table_one also sets use_internal_variance to false. However, looking through other code in the Phenix tree, there are some instances where use_internal_variance is set to false with no option to change it, so we will double check if that is the behavior that we want. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Tue, Nov 1, 2016 at 7:06 AM, Keitaro Yamashita

wrote:

Dear Richard,

Thanks a lot. I hope some Phenix developer will make a comment.

Best regards, Keitaro

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Dear Keitaro,

I've made the change you suggested in merging_statistics.py - it looks

2016-11-01 20:19 GMT+09:00 : like an oversight, which didn't affect xia2 since we are always calculating merging statistics given an scaled but unmerged mtz file, never an XDS or scalepack-format file.

...

As to what defaults Phenix uses, that is better left to one of the

Phenix developers to comment on.

...

Cheers,

Richard

Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078

Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE

________________________________________ From: [email protected] [cctbxbb-bounces@phenix-

...

Sent: 01 November 2016 10:41 To: cctbx mailing list Subject: Re: [cctbxbb] use_internal_variance in iotbx.merging_statistics

Dear Richard and everyone,

Thanks for your reply. What kind of input do you give to iotbx.merging_statistics in xia2? For example, when XDS file is given, use_internal_variance=False is not passed to merge_equivalents() function. Please look at the lines of filter_intensities_by_sigma.__init__() in iotbx/merging_statistics.py. When sigma_filtering == "xds" or sigma_filtering == "scalepack", array_merged is recalculated using merge_equivalents() with default arguments.

If nobody disagrees, I would like to commit the fix so that use_internal_variance variable is passed to all merge_equivalents() function calls.

I am afraid that the behavior in the phenix-1.11 would be confusing. In phenix.table_one (mmtbx/command_line/table_one.py), use_internal_variance=False is default. This will be OK with the fix I suggested above.

Can it also be default in phenix.merging_statistics, not to change the program behavior through phenix versions?

Best regards, Keitaro

2016-11-01 18:21 GMT+09:00 :

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Dear Keitaro,

iotbx.merging_statistics does have the option to change the parameter use_internal_variance. In xia2 we use the defaults use_internal_variance=False, eliminate_sys_absent=False, n_bins=20, when calculating merging statistics which give comparable results to those calculate by Aimless:

$ iotbx.merging_statistics Usage: phenix.merging_statistics [data_file] [options...]

Calculate merging statistics for non-unique data, including R-merge, R-meas, R-pim, and redundancy. Any format supported by Phenix is allowed, including MTZ, unmerged Scalepack, or XDS/XSCALE (and possibly others). Data should already be on a common scale, but with individual observations unmerged. Diederichs K & Karplus PA (1997) Nature Structural Biology 4:269-275 (with erratum in: Nat Struct Biol 1997 Jul;4(7):592) Weiss MS (2001) J Appl Cryst 34:130-135. Karplus PA & Diederichs K (2012) Science 336:1030-3.

Full parameters:

file_name = None labels = None space_group = None unit_cell = None symmetry_file = None high_resolution = None low_resolution = None n_bins = 10 extend_d_max_min = False anomalous = False sigma_filtering = *auto xds scala scalepack .help = "Determines how data are filtered by SigmaI and I/SigmaI. XDS" "discards reflections whose intensity after merging is less

...

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"-3*sigma, Scalepack uses the same cutoff before merging,

and"

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"SCALA does not do any filtering. Reflections with negative

SigmaI"

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"will always be discarded." use_internal_variance = True eliminate_sys_absent = True debug = False loggraph = False estimate_cutoffs = False job_title = None .help = "Job title in PHENIX GUI, not used on command line"

Below is my email to Pavel and Billy when we discussed this issue by

email a while back:

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The difference between use_internal_variance=True/False is explained

in Luc's document here:

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libtbx.pdflatex $(libtbx.find_in_repositories cctbx/miller)/equivalent_

reflection_merging.tex

...

Essentially use_internal_variance=False uses only the unmerged sigmas

to compute the merged sigmas, whereas use_internal_variance=True uses instead the spread of the unmerged intensities to compute the merged sigmas. Furthermore, use_internal_variance=True uses the largest of the variance coming from the spread of the intensities and that computed from

...

...

https://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/

cctbx/miller/merge_equivalents.h#l379

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Aimless has a similar option for the SDCORRECTION keyword, if you set

...

...

http://www.mrc-lmb.cam.ac.uk/harry/pre/aimless.html#sdcorrection

"SAMPLESD is intended for very high multiplicity data such as XFEL

serial data. The final SDs are estimated from the weighted population variance, assuming that the input sigma(I)^2 values are proportional to the

...

...

I think that the "external" variance is probably better if the sigmas

from the scaling program are reliable, or for low multiplicity data. For high multiplicity data or if the sigmas from the scaling program are not reliable, then "internal" variance is probably better.

...

Cheers,

Richard

Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078

Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE

________________________________________ From: [email protected] [cctbxbb-bounces@phenix-

online.org] on behalf of Keitaro Yamashita [[email protected]]

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Sent: 01 November 2016 07:23 To: cctbx mailing list Subject: [cctbxbb] use_internal_variance in iotbx.merging_statistics

Dear Phenix/CCTBX developers,

iotbx/merging_statistics.py is used by phenix.merging_statistics, phenix.table_one, and so on. By upgrading phenix from 1.10.1 to 1.11, merging statistics-related codes were significantly changed.

Previously, miller.array.merge_equivalents() was always called with argument use_internal_variance=False, which is consistent with XDS, Aimless and so on. Currently, use_internal_variance=True is default, and cannot be changed by users (see below).

These changes were made by @afonine and @rjgildea in rev. 22973 (Sep 26, 2015) and 23961 (Mar 8, 2016). Could anyone explain why these changes were introduced?

https://sourceforge.net/p/cctbx/code/22973 https://sourceforge.net/p/cctbx/code/23961

My points are:

- We actually cannot control use_internal_variance= parameter because it is not passed to merge_equivalents() in class filter_intensities_by_sigma.

- In previous versions, if I gave XDS output to phenix.merging_statistics, values calculated in the same way (as XDS does) were shown; but not in the current version.

- For (for example) phenix.table_one users who expect this behavior, it can give inconsistency. The statistics would not be consistent with the data used in refinement.

cf. the related discussion in cctbxbb: http://phenix-online.org/pipermail/cctbxbb/2012-October/000611.html

Best regards, Keitaro _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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online.org] on behalf of Keitaro Yamashita [[email protected]] than" the unmerged sigmas. As a result, use_internal_variance=True can only ever give lower I/sigI than use_internal_variance=False. The relevant code in the cctbx is here: the option SAMPLESD, which I think is equivalent to use_internal_variance=True. The default behaviour of Aimless is equivalent to use_internal_variance=False: true errors. This probably gives a more realistic estimate of the error in <I>. In this case refinement of the corrections is switched off unless explicitly requested." the e-mail. transmitted in or with the message.

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