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[Imgcif-l] Progress on a CCTBX imgCIF reader
- To: imgcif-l@iucr.org
- Subject: [Imgcif-l] Progress on a CCTBX imgCIF reader
- From: Nicholas Sauter <nksauter@lbl.gov>
- Date: Mon, 9 Aug 2010 14:53:16 -0700
- Cc: r.j.gildea@durham.ac.uk, "Ralf W. Grosse-Kunstleve" <rwgk@cci.lbl.gov>, luc_j_bourhis@mac.com
We have some progress to report on implementing an imgCIF reader within the Computational Crystallography Toolbox (cctbx; see http://cctbx.sf.net). I've written a quick script to show that a Python-based CIF parser from Richard Gildea can be combined with CBF byte offset decompression from Graeme Winter, allowing us to read an ADSC/CBF macromolecular dataset with a Python script. The short test script is located in the cctbx source bundle: cctbx_project/iotbx/detectors/tst_py_cbf.py It is encouraging that the turnaround time for decompressing a single 3072x3072 image is about 70ms on our Linux server; number crunching is done with compiled Python extensions. As background, the cctbx package already provides a wrapper for the Bernstein/Ellis imgCIF library, so the functionality we've implemented isn't new. What is new is that at least part of the imgCIF standard can be encoded in Python independently and in a rapid fashion, and we argue that this should encourage the more widespread use of the standard. The program tst_py_cbf.py gives just the minimum function set necessary to process the data. It will become more useful if others contribute to the open source project; for example, a CBF writer is readily within reach. The supplied code (tst_py_cbf.py) also has a validation function comparing the Python-based read results with those obtained from the Bernstein/Ellis library. Thanks to Richard Gildea for supplying the Python-based CIF parser in the iotbx.cif module; Ralf Grosse-Kunstleve for creating the CCTBX framework; Graeme Winter for supplying an example thaumatin dataset from Diamond Light Source, and Chris Nielson for implementing the CBF format for ADSC images. One further note: the dataset in question, in CBF format, processes correctly in both MOSFLM 7.0.6 (data reduction) and LABELIT (autoindexing). Both of these programs link to the Bernstein/Ellis library. Nick Sauter, LBNL _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
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