*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
There is a new development release of buccaneer out today for Linux/x86 and Mac/ppc, with a number of improvements. The new features are described below, but first I need to cover a few details about the new release process. From ccp4 release 6.0.2, which will be available shortly, there will be two buccaneer versions available. The 'stable' version will be available from ccp4 as an optional package when you do your ccp4 install. This is currently buccaneer version 0.4.2, and will be available for a variety of platforms. The 'development' version will be available from York, and will contain all the latest features, but will only be available for Linux/x86 and Mac/ppc. Today's development version is 0.5.0, however I expect to put out a new release every month or two. The two versions can both be installed at once: they will have separate program files and GUIs. So you can install both and run which ever one you prefer. The new features in 0.5.0 over 0.4.2 are as follows: 1. There is now an automated install script. Simply unpack the tar file, 'cd' into the buccaneer directory, and run the 'install.sh' shell script. 2. Chain growing has been improved, by implementing a more robust test for how far to grow the chain. This has increased the accuracy of the resulting chains somehwat, and provides more consistent behavious across different structures. 3. Sequencing now tests for single residue register errors (where a resisude has been skipped or an extra one inserted) in the chain trace, and adjust the sequence to mark the error. This leads to a signficant increase in the amount of chain sequenced. 4. Sequencing also attempts to identify disjoint sequences - where a single chain trace contains several separate sections of the true sequence due to wrong connectivity. This provides a small addition increase in the amount of chain sequenced. I hope to improve this further, and eventually to use it to correct connectivity. 5. A new stage has been added: 'correction'. This stage will automatically rebuild the chain where a register error of one or two residues has occured. 6. You can now set a resolution limit in the GUI. The default cutoff is 2.0A - much beyond this doesn't improve building signfiicantly but does make the calculation slower, but you can change this value if you wat. 7. A new reference structure (1tqw) is provided and is now the default. This structure provides a better sampling of side chain conformations, and thus is better for sequencing. The development version of Buccaneer is available here: http://www.ysbl.york.ac.uk/~cowtan/buccaneer/buccaneer.html Kevin
