The new version of Modeller, 8v1, is now available for download from http://salilab.org/modeller/.
If you have a license key for Modeller 8v0 or 7v7, there is no need to reregister for Modeller 8v1 - the same license key will work. (It won't do any harm to reregister if you want to, though!)
If you encounter bugs in Modeller 8v1, please see http://salilab.org/modeller/manual/node11.html for information on how to report them.
New features in Modeller 8v1 include:
# Removal of limits on the number of pseudo atoms, segments, the length of file names and most other strings, and the number of parameters in parameter files.
# Removal of the read_restyp() command. To read a user-defined residue type file, set restyp_lib_file when creating an environ object.
# Bug fix: the correct VDW radii (as selected by topology.submodel) are now used for PSA calculations (previously the all-hydrogen radii were used in all cases).
# Improved error handling: almost all errors should be recoverable now (using the standard Python exception handling mechanism) and incorrect input should trigger an error rather than causing Modeller to crash (please report any crashes as bugs to the developers).
# SALIGN bug fixes, improved binning of access classes.
# Modeller scripts are now more like 'real' Python scripts; the PYTHONPATH environment variable is honored, and additional command line arguments can be given to your scripts (accessible as sys.argv).
# Bug fix for alignment.segment_matching(): correct alignment scores are now written.
# Support for AMD64 and EM64T (Opteron/Xeon64) Linux machines.
# DOPE model assessment now returns only the DOPE energy itself by default, ignoring other energy terms.
# Bug fix for model.restraints.pick() when used with absolute position restraints; always allow 1-atom restraints to pass the residue_span_range check.
Ben Webb, Modeller Caretaker