[buster-discuss] Using aB_deposition_combine before deposition to PDB

[BUSTER Developers]

Dear Laurent,

On Sat, Feb 11, 2023 at 04:51:48PM +0100, Laurent wrote:
> I would like to prepare files for PDB deposition after data
> processing with autoProc and refinement with buster.

Yes.

> I use aB_deposition_combine in order to combine informations from
> reflection files from autoProc and buster.

Correct.

> Howewer, I only get NOTEs about � too few matches found � and no
> files are produced. See the transcript below. Do I miss something in
> the usage of the command?

Your usage is correct:

  aB_deposition_combine -aP ./process_03/  ./refine_08/BUSTER_model.cif ./refine_08/BUSTER_refln.cif

Let's discuss what that tool is then actually trying to do: for each
reflection data block within the multi-block mmCIF files produced by
autoPROC (which it tries to find within the directory given by the -aP
flag), it will try and match up reflections with those reported by
BUSTER (in BUSTER_refln.cif). The assumption is that the autoPROC
result files in "./process_03/" were used without any major
modification as input to BUSTER - e.g. the MTZ file
"staraniso_alldata-unique.mtz".

However, that might not have been the case here: if you e.g. used
intermediate data (unscaled or even scaled intensities) with some
other scaling program or a different procedure to go from intensities
to amplitudes, the amplitudes in BUSTER_refln.cif (describing the data
as input into refinement) will be different from those in
e.g. Data_1_autoPROC_STARANISO_all.cif.

You can see in the log file at

  NOTE : found 32/100 in
         ./process_03//Data_1_autoPROC_STARANISO_all.cif
         (1_staraniso)

  NOTE : too few matches found

that there are some matching amplitude/sigma pairs found - but not
quite enough (only 32 out of 100). Maybe some other changes
(re-indexing/scaling? SG assignment changed?) occured between the
autoPROC job and the final BUSTER refinement?

You can change some of the decision making e.g. by running

  aB_deposition_combine \
    autoBUSTER_DepositionCombine_FindProcessingCif_RandomHit=0.2 \
    ...

to allow for further analysis even if only 20% of the initial
comparisons (between 100 random reflections) are successful. Or
increase the

  autoBUSTER_DepositionCombine_FindProcessingCif_RandomFuz

parameter (default = 0.02) to allow for more difference between
amplitudes. However, you should also double check if ./process_03/ is
the autoPROC result directory containing the actually used reflection
data that went into BUSTER.

Another potential problem can be so-called daisy-chaining of
reflection data - e.g. taking the staraniso_alldata-unique.mtz from
autoPROC into MR, then the output MTZ file from that MR step into
refinement program A and the resulting output MTZ file into refinement
with program B. That is always a recipe for confusion with potential
data modification or rescaling happening.

In our hands, if e.g. the staraniso_alldata-unique.mtz file was taken
as-is for refinement you should then see 100/100 reflections matching
and the tool creating the final combined versions without any problem.

Does that make sense?

Cheers

Clemens, Claus & Gerard

> Process_03 is the folder produced by autoProc (-d process_03). Running with -aP ./process_03/Data_1_autoPROC_STARANISO_all.cif does not help. 
> 
> (base) % aB_deposition_combine -aP ./process_03/  ./refine_08/BUSTER_model.cif ./refine_08/BUSTER_refln.cif 
> 
>  ##############################################################################
>  # This software is licenced to : Centre Natinonal de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale 
>  ##############################################################################
> 
>  ##############################################################################
>  ##   [aB_deposition_combine] Tool to help combining mmCIF files for PDB deposition
>  ##############################################################################
> 
>       Copyright (C) 1992-2022 by Global Phasing Limited
>  
>                 All rights reserved.
>  
>                 This software is proprietary to and embodies the confidential
>                 technology of Global Phasing Limited (GPhL). Possession, use,
>                 duplication or dissemination of the software is authorised
>                 only pursuant to a valid written licence from GPhL.
> 
>       Version:  2.10.4  <2022-06-08 01:47:47>
> 
>  ------------------------------------------------------------------------------
> 
>     Reference:  Bricogne G, Blanc E, Brandl M, Flensburg C, Keller P,
>                 Paciorek W, Roversi P, Sharff A, Smart O, Vonrhein C,
>                 Womack T (2022). BUSTER version 2.10.4. Cambridge, United
>                 Kingdom: Global Phasing Ltd.
>  
>       Authors:  (2020-2021) Bricogne G, Flensburg C, Keller P, Vonrhein C, Wojdyr M
> 
>  
>       Contact:  buster-develop at GlobalPhasing.com
>  
>  ==============================================================================
>  
>  
>  NOTE : found 32/100 in
>         ./process_03//Data_1_autoPROC_STARANISO_all.cif
>         (1_staraniso)
>  
>  
>  NOTE : too few matches found
>  
>  
>  NOTE : found 0/100 in
>         ./process_03//Data_1_autoPROC_STARANISO_all.cif
>         (1_staraniso_early)
>  
>  
>  NOTE : too few matches found
>  
>  
>  NOTE : found 0/100 in
>         ./process_03//Data_1_autoPROC_STARANISO_all.cif
>         (1_staraniso_late)
>  
>  
>  NOTE : too few matches found
>  
>  
>  NOTE : found 0/100 in
>         ./process_03//Data_2_autoPROC_TRUNCATE_all.cif
>         (2_truncate)
>  
>  
>  NOTE : too few matches found
>  
>  
>  NOTE : found 0/100 in
>         ./process_03//Data_2_autoPROC_TRUNCATE_all.cif
>         (2_truncate_early)
>  
>  
>  NOTE : too few matches found
>  
>  
>  NOTE : found 0/100 in
>         ./process_03//Data_2_autoPROC_TRUNCATE_all.cif
>         (2_truncate_late)
>  
>  
>  NOTE : too few matches found
>  
> 
>  Normal termination (31 sec)