Serial Femtosecond Crystallography of G Protein-Coupled Receptors
Vadim Cherezov has made available the Cheetah preprocessed images, formated for use with CrystFEL, used in their latest Science paper on the structure of the 5-HT2B receptor bound to ergotamine grown in lipidic cubic phase.
You can obtain the data from the ID 21 page.
De novo protein crystal structure determination from X-ray free-electron laser data
LCLS XTC raw data for High-Resolution Protein Structure Determination by SFX uploaded
Sébastien Boutet has made available the XTC files related to CXIDB entry ID 17, and they are now available for download.
You can download them from the ID 17 raw data page. Please bear in mind that the files are stored on tape so it can take several minutes for the server to reply to a download request.
Nature announces Scientific Data, to help publish discover and reuse research data
Nature Publishing Group will next spring launch Scientific Data, an open-access, online-only journal for detailed descriptions of data sets.
I think this provides a great opportunity to reward researches with data to publish but who have difficulties publishing a suitable reference to it, given them a change to receive the proper acknowledgement they deserve.
For more details please check the announcement.
Single-particle structure determination by correlations of snapshot X-ray diffraction patterns
ID-20 has just been made available. It contains the data pertaining to the paper by D. Starodub et al. Single-particle structure determination by correlations of snapshot X-ray diffraction patterns, Nature Communications, December 2012.
CXIDB paper published
I have authored a short paper about CXIDB F. Maia The Coherent X-ray Imaging Data Bank, Nature Methods, August 2012. It has been published a while ago I forgot to announce it here!
Please cite this reference when you make of of the database.
One more dataset
A dataset from the article A. V. Martin et al., Femtosecond dark-field imaging with an X-ray free electron laser, Optics Express, June 2012 was kindly deposited.
It describes a new interesting technique for recovering as much information as possible from diffraction patterns with missing data.
The new dataset was given ID-19.
Fractal morphology dataset deposited
You can find them under ID-16.
Two new datasets deposited
Two new datasets have just been published, one obtained using serial femtosecond crystallography and a second one using X-ray projection imaging on randomly oriented mask.
The first one dataset comes from the article by Sébastien Boutet et al., High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography, Science, May 2012.
The second dataset correspond to the data from the article Hugh T. Philipp et al., Solving structure with sparse, randomly-oriented x-ray data, Optics Express, June 2012.
You can find them under ID-17 and ID-18 respectively.
CXI version 1.3 released
The biggest change is the introduction of the concept of scans to accomodate datasets where one experimental parameter is continuously changed such as wavelength or sample rotation. A new axes attribute was introduced, related with scans. The ptychography example was updated, and now makes use of scans. Several small corrections and clarifications. As usual the document can be found on github.
A new software page and the public release of CrystFEL.
The public release of CrystFEL spurred me to finally create a page dedicated to software useful for CXI experiments. You can find it under Resources.
CrystFEL was published by Thomas White et al. in a paper entitled CrystFEL: a software suite for snapshot serial crystallography in latest issue of the J. of Appl. Crystallography. This software makes it possible to analyze data from serial femtosecond nanocrystallography experiments like that described in Femtosecond X-ray protein nanocrystallography by Henry Chapman et al.
You can obtain it at http://www.desy.de/~twhite/crystfel.
Recent paper in Nature argues for open computer programs.
D. Ince, L. Hatton and J. Graham-Cumming have published an interesting perspective in Nature entitled The case for open computer programs.
In it they argue that the full release of the source code of software involved in scientific publications is as important as releasing the experimental data. One of the major argument for it are that it provides an exact description of the algorithm used, enabling reproducibility.
This is an important subject and I'm glad it's receiving greater attention.
Paper describing previously deposited LCLS dataset published
S. Kassemeyer et al. have recently published Femtosecond free-electron laser x-ray diffraction data sets for algorithm development, in Optics Express, describing in detail the dataset from LCLS that has been previously deposited.
This dataset corresponds to IDs 10 to 14 and their records have now been updated to reflect the publication.
3D X-ray diffraction imaging dataset deposited
125 diffraction images of a silicon nitride pyramid sprinkled with gold balls, taken at different tilts, 1 degree appart have just been deposited. These are the experimental data used in the article Chapman, H.N. et al. High-resolution ab initio three-dimensional x-ray diffraction microscopy, Journal of the Optical Society of America A, 23, 1179-200, May 2006.
You can find it here.
Raw data from LCLS dataset available online
The raw data corresponding to IDs 10 to 14, the large LCLS dataset recently deposited is now available online.
The files are in XTC format, the native LCLS format, and they are very large so we recommend that you use a dedicated program to download them, not a web browser. If you plan to download a large fraction of the data please contact us so we can arrange a more efficient method.
The data can be accessed from a link at the bottom of each entry.
Missing pixels in LCLS dataset
There was an error during the conversion of the LCLS dataset which caused one row of pixels to be missing. This has now been corrected. If you have datasets with 511 pixels in one dimension please download them again. Thanks to Chun Yoon for pointing it out.
Large LCLS dataset deposited
Five datasets containing selected runs from two LCLS experiments, AMO15010 and AMO10510 have been added to the data bank. The datasets contain diffraction images of nanorice, magnetosomes, TMV, T4 and PBCV.
You can find the links from the Browse Data page as usual.
Nanorice data from FLASH experiments deposited
A large number of diffraction images from iron oxide ellipsoids (often referred to as nanorice) have been deposited. These include the images used in the article N. D. Loh et al., Cryptotomography: reconstructing 3D Fourier intensities from randomly oriented single-shot diffraction patterns, Phys Rev Lett., 104, 225501, June 2010
Labeled Yeast data added to the Data Bank
The data used in the article Johanna Nelson et al., High-resolution x-ray diffraction microscopy of specifically labeled yeast cells, PNAS, 16, 7235-7239, April 2010, has been added to the data bank. Five different tilts of the same sample correspond to IDs 4 through 8. ID 4 also includes the reconstructed image.
You can access them through the Browse Data page.
CXI file format updated
New entry in the database
The data corresponding to the first experimental demonstration of the diffraction before destruction concept, has been added to the database.
The group, which presented their findings in the article Henry N. Chapman et al., Femtosecond diffractive imaging with a soft-X-ray free-electron laser, Nature Physics, 2, 839-843, November 2006, has now deposited the data which was assigned ID 3.
Science highlights data access and organization
Science has recently published a special issue entitled "Dealing with Data".
The issue (which is available for free), focus on the challenges posed by the current data deluge, including the difficulty in managing and organizing such large data quantities as well as the wasted effort in data duplication due to the lack of funding for preserving data.
I think this is both highly relevant to this website and well worth a read.
Mimi virus data inaugurates the Data Bank
The data corresponding to the background corrected data and configuration files used in the article M. Marvin Seibert, Tomas Ekeberg, Filipe R. N. C. Maia et al., Single mimivirus particles intercepted and imaged with an X-ray laser, Nature, 470, 78-81, February 2011, are the first two entries in the data bank, with IDs 1 and 2.
You can also access them through the Browse Data page.