Quality Control: Difference between revisions

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This is an attempt of putting together a number of datasets with different characteristics (high and low resolution, good and bad crystals, untwinned and twinned), their evaluation with different versions of [[XDS]] up to the structure solution (as far as that can be done automatically), and the determination of the quality of the resulting data using experimental phasing and refinement.
This is an attempt of putting together a number of datasets with different characteristics (high and low resolution, good and bad crystals, untwinned and twinned), their evaluation with different versions of [[XDS]] up to the structure solution (as far as that can be done automatically), and the determination of the quality of the resulting data using experimental phasing and refinement.


The '''goal''' of this is to find generally optimal parameters for XDS data reduction, to compare new versions of [[XDS]] with older ones, and to discover bugs or regressions. At the same time, it serves to display standard procedures for solving crystal structures, which may be used for teaching or learning crystallography.
== Assorted projects ==
 
The '''metrics''' I would like to look at is
* anomalous signal: SHELXC anomalous correlations (internally or between wavelengths); SHELXD (fixed version) success rates and CCall/CCweak maximum values. Clemens Vonrhein additionally suggested anomalous difference fourier peak heights.
* refinement of a given (known) set of heavy atom positions in (e.g.) SHARP (fixed version): r.m.s. or absolute phase difference, or map correlation w.r.t. phases from good model
* refinement with (e.g.) refmac5 (fixed version) of a given model, finding LL and R/R<sub>free</sub>


For each project mentioned below, both '''the raw data ''and'' the [[XDS]] data reduction is available''' - links are on the project pages, which are named according to their [http://www.rcsb.org PDB] ids.  
For each project mentioned below, both '''the raw data ''and'' the [[XDS]] data reduction is available''' - links are on the project pages, which are named according to their [http://www.rcsb.org PDB] ids.  
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* 2-wl Bromide MAD: PDB id [[1RQW]] ([http://www.rcsb.org/pdb/explore.do?structureId=1RQW Thaumatin], a sweet-tasting protein of 207 resides, spacegroup P4<sub>1</sub>2<sub>1</sub>2, resolution 1.8 Å, collected at the DGK Workshop 2007; could also treat either peak or inflection as SAD. These datasets have been made available by Manfred S. Weiss and Annette Faust (see [http://www.embl-hamburg.de/Xray_Tutorial/ Xray Tutorial]).
* 2-wl Bromide MAD: PDB id [[1RQW]] ([http://www.rcsb.org/pdb/explore.do?structureId=1RQW Thaumatin], a sweet-tasting protein of 207 resides, spacegroup P4<sub>1</sub>2<sub>1</sub>2, resolution 1.8 Å, collected at the DGK Workshop 2007; could also treat either peak or inflection as SAD. These datasets have been made available by Manfred S. Weiss and Annette Faust (see [http://www.embl-hamburg.de/Xray_Tutorial/ Xray Tutorial]).


== ACA2011 ==


As part of the 2011 ACA workshop on data processing, organized by Ed Collins, I additionally document XDS data processing of
As part of the [http://bl831.als.lbl.gov/example_data_sets/ACA2011/DPWTP-website/index.html 2011 ACA workshop on data processing], organized by Ed Collins and Andy Torelli, I extensively document XDS data processing (and in most cases also structure solution) of
* [[2VB1]]: hen egg-white lysozyme @ 0.65Å resolution, PDB id [http://www.rcsb.org/pdb/explore/explore.do?structureId=2VB1 2vb1]. Data (sweeps a to h, each comprising 60 to 360 frames of 72MB) were collected by Zbigniew Dauter at APS 19-ID and are available from [http://bl831.als.lbl.gov/example_data_sets/APS/19-ID/2vb1/ here]. Details of data collection, processing and refinement are [http://journals.iucr.org/d/issues/2007/12/00/be5097/index.html published].  
* [[2VB1]]: hen egg-white lysozyme @ 0.65Å resolution, PDB id [http://www.rcsb.org/pdb/explore/explore.do?structureId=2VB1 2vb1]. Data (sweeps a to h, each comprising 60 to 360 frames of 72MB) were collected by Zbigniew Dauter at APS 19-ID and are available from [http://bl831.als.lbl.gov/example_data_sets/APS/19-ID/2vb1/ here]. Details of data collection, processing and refinement are [http://journals.iucr.org/d/issues/2007/12/00/be5097/index.html published].  
* [[simulated-1g1c]]: James Holton's simulated (using his MLFSOM) data of PDB id [http://www.rcsb.org/pdb/explore/explore.do?structureId=1G1C 1g1c] - 100 synthetic datasets (15 frames each) strongly affected by radiation damage. These 100 datasets were simulated in random orientations and with random (?) "crystal" sizes. The processing and scaling can be considered non-standard, and challenging.
* [[simulated-1g1c]]: James Holton's simulated (using his MLFSOM program) data of PDB id [http://www.rcsb.org/pdb/explore/explore.do?structureId=1G1C 1g1c] - 100 synthetic datasets (15 frames each) strongly affected by radiation damage. These 100 datasets were simulated in random orientations and with random (?) "crystal" sizes. The processing and scaling can be considered non-standard, and challenging.
* [[2QVO]]: S-SAD: PDB id [http://www.rcsb.org/pdb/explore.do?structureId=2QVO AF1382], a 95-residue protein used by James Tucker Swindell II to establish optimized procedures for data reduction. The data available to solve the structure are two runs of 360° collected at 1.9Å wavelength.
* [[2QVO]]: S-SAD: PDB id [http://www.rcsb.org/pdb/explore.do?structureId=2QVO AF1382], a 95-residue protein used by James Tucker Swindell II to establish optimized procedures for data reduction. The data available to solve the structure are two runs of 360° collected at 1.9Å wavelength. Datasets are at [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/2qvo/].
* [[3CSL]]: 3-wl SeMet-MAD data PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL], a complex of a 22 stranded beta-barrel outer membrane protein (the ordered residues 112-865 harbour 9 SeMet), its 173-residue hemophore (1 SeMet), and heme. Datasets are at [ftp://turn5.biologie.uni-konstanz.de/pub/datasets/]. 2 complexes per ASU, useful data to 3.2Å, useful anomalous data to about 5Å. Challenging for humans, and too difficult for automatic methods of structure solution and model building.
* [[3CSL]]: 3-wl SeMet-MAD data PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL], a complex of a 22 stranded beta-barrel outer membrane protein (the ordered residues 112-865 harbour 9 SeMet), its 173-residue hemophore (1 SeMet), and heme. Datasets are at [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/3csl]. 2 complexes per ASU, useful data to 3.2Å, useful anomalous data to about 5Å. Challenging for humans, and too difficult for automatic methods of structure solution and model building.
* [[1Y13]]: SAD with a twist that requires some detective work.
 
== [[ACA2014]] ==
 
Data from several projects were processed by experts at the "Data processing with the pros" session of the [[ACA2014]] in Albuquerque, New Mexico (USA) at the end of May 2014. [http://bl831.als.lbl.gov/example_data_sets/ACA2011/DPWTPreloaded/index.html This website] has detailed descriptions and links.
 
== Simulated data ==


Recently I've written [[SIM_MX]] which should make parts of testing and development of XDS independant from real data.
I wrote [[SIM_MX]] which makes testing and development of XDS independant from real data.
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