The objective of this core TR&D project is to extend the power and improve the ease of use of software tools used for molecular microscopy.
The specific aims are: (1) to make the interchange of image data between packages seamless and transparent to the user. (2) to add a number of tools and procedures to the SUPRIM software package aimed at streamlining helical reconstructions. (3) Set up procedures which are aimed at automating or semi-automating complex image processing problems. (4) Develop a user interface for these processing tasks which provides for windows and menu selectable items will be available to connect to the most common procedures. (5) Port those sections of the procedures which are clearly identifiable as consuming large amounts of CPU time to run on fast machines. Nearly all of these aims have now been achieved: Briefly, structure determination by electron microscopy can be classified into four categories based on the symmetry of the object being reconstructed. These four methods are helical reconstruction (l-D symmetry), crystal reconstruction (2-D or 3-D symmetry), icosahedral reconstruction (60 fold symmetry as in viruses) and single particle reconstruction (no symmetry). There are corresponding software packages that are specifically designed for each of these reconstruction methods. At the NCMIR, we have available SUPRIM for single particle reconstruction, PHOELIX for helical reconstruction and the MRC based crystallographic reconstruction package (SPECTRA, ICE, Origtilt, Latline as well as the CCP4 crystallographic package). We have made several improvements to the molecular microscopy software. First, Dr. Carragher has finished a complete revision of SUPRIM in ANSI C in order to standardize the package and therefore, make it portable to other platforms. This new version of SUPRIM (vS.i) is also able to read MRC data format. Second, Dr. Carragher has rewritten the original MRC helical package for processing of helical particles into a new system of programs called PHOELIX. She has also written shell scripts for semi-automated processing of helical filaments in order to speed the data processing. Third, Dr. Sosinsky has installed the MRC/CCP4 crystallographic packages and will show the gap junction hemichannel structure that she and Dr. Perkins have determined that was done on the NCMIR computers. Packages are also available for icosahedral reconstruction that may be installed at a later time. In this way, we can service the community by having all types of molecular microscopy codes available for use should a need arise.
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