Changes since release 6v2

• The CUT_OVERHANGS argument to the WRITE_ALIGNMENT command has been removed, and replaced by a more powerful EDIT_ALIGNMENT command.

• The MAX_LOOP_LENGTH argument to the PICK_ATOMS command has been replaced by MINMAX_LOOP_LENGTH, such that both the minimum and maximum loop segment lengths can be selected for in 'SEGMENT' mode.

• The SEARCH_CHAINS_LIST and SEARCH_CHAINS_FILE arguments to SEQUENCE_SEARCH have been removed. Instead, a sequence database must now be read into memory prior to using SEQUENCE_SEARCH by using the new READ_SEQUENCE_DB command. (Such a database can also be written out with WRITE_SEQUENCE_DB.)

• New 'all-hydrogens' example directory, for building all-hydrogen models.

• CHARMM topology libraries are now PDB (IUPAC) compliant. Most obviously, this has resulted in the following name changes:
  • The HSD (neutral histidine) residue is now HIS.
  • The ILE CD atom is now CD1.
  • The LEU CD1 and CD2 atoms have been swapped.
  • PDB hydrogen atom naming conventions now apply.
  See also the 'top-charmmH.lib' file for the old CHARMM-style naming, and the comments at the start of 'top.lib'.

• READ_ALIGNMENT can now read 'FASTA' format alignments. Additionally, the CLOSE_FILE, REWIND_FILE, and END_OF_FILE variables can be used to read partial 'PIR' or 'FASTA' files.

• MALIGN3D allows the filenames of fitted atom files to be customized with the EDIT_FILE_EXT variable.

• MAKE_RESTRAINTS can now impose additional gap-distance weighting on distance restraints, using the RESTRAINT_STDEV2 variable.

• New commands for dealing with profiles: ALN_TO_PROF, PROF_TO_ALN, WRITE_PROFILE, READ_PROFILE, BUILD_PROFILE.

• New options to ALIGN and ALIGN2D for dealing with profiles: WEIGH_SEQUENCES, SMOOTH_PROF_WEIGHT, READ_PROFILE, INPUT_PROFILE_FILE, WRITE_PROFILE, OUTPUT_PROFILE_FILE. ALIGN_WHAT can also now take the value 'PROFILE'.

• Other new commands: SEQFILTER, TIME_MARK, MAKE_CHAINS, VOLUME, VOLUME_CAVITY.