The new version of Modeller, 9v4, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information.
If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9v4 - the same license key will work. (It won't do any harm to reregister if you want to, though!)
9v4 is primarily a bugfix release relative to the last public release (9v3). Major user-visible changes include:
# The speed of GB/SA calculations has been dramatically increased. # io_data.atom_files_directory is now a Python list of directories, rather than a colon-separated string. (This is so that everything works on Windows, where ':' is a valid character in directory names.) Old scripts that use colon-separated strings should still work, but will trigger a warning. # When reading or writing compressed files, the uncompressed versions of these files are now written into writeable local storage. Previously, these files were written into the same directory as the compressed versions, which is problematic when that directory is read-only or is on network storage. # Update PDB files used in the examples (remediated PDBs are now used).
See the Modeller manual for a full change log: http://salilab.org/modeller/9v4/manual/node38.html
If you encounter bugs in Modeller 9v4, please see http://salilab.org/modeller/9v3/manual/node10.html for information on how to report them.
Ben Webb, Modeller Caretaker