Modeller 9.16 release 01-12-2016:
  - alignment.check_sequence_structure() no longer erroneously warns about
    the potentially large CA-CA distances between residues in different
    chains.
  - Add Python 3.5 support.
  - Bundled version of HDF5 updated to 1.8.14.
  - Bugfix: process file xxx.c.pdb as a PDB file, not mmCIF.
  - Bugfix: alignment.write() no longer fails on Python filelike objects.
  - Bugfix: under some circumstances, overriding loopmodel.special_patches()
    would cause coordinates to be incorrectly assigned and/or a "list index
    out of range" error.
  - Bugfix: in certain badly-performing optimizations, the nlogn nonbond pair
    generation function would use all system memory. It is now capped at
    approximately 200MiB, controllable with the energy_data.max_nlogn_grid_cells
    parameter.

Modeller 9.15 release 05-19-2015:
  - Warn if 'structureX' is mistyped in alignment file header.
  - The "RTF restraint not found" warning is now suppressed for the common
    case of failing to make a peptide bond (and the associated improper)
    to the next residue at the end of a chain.
  - Suppress making peptide bond (and the associated improper) to HETATMs
    unless they appear to be modified amino acids (they have a carbon CA
    atom).
  - Bundled version of HDF5 updated to 1.8.13.
  - Bugfix: pad 4-digit residue numbers correctly for PDB output.

Modeller 9.14 release 07-29-2014:
  - The new PDB format (PDBx/mmCIF) is now handled. Templates can be mmCIF
    files, and model.read() and model.write() also support mmCIF. See also
    automodel.set_output_model_format() to write out models in mmCIF format.
  - automodel-generated PDB or mmCIF files now contain extra header
    information, including the names of the sequence and template(s) and the
    values of any assessment scores.
  - Add Python 3.4 support.
  - Add support for 64-bit Windows.
  - density.read() now uses the origin in the MRC/CCP4 file if it is not
    specified.
  - Bundled version of HDF5 updated to 1.8.11.
  - Bugfix: Don't generate invalid format PDB files when biso <= -100.
  - Bugfix: don't crash on reading an empty PSSM database.
  - Bugfix: don't crash in model.to_iupac() if the residues to be modified
    are missing sidechains or are not really amino acids (e.g. BLK residues).
  - Bugfix: fix corruption of nonbonded list if selection.energy() is called
    from within an optimizer action.
  - Bugfix: use 64-bit integers to track memory usage to avoid overflows in
    the 'Dynamically allocated memory' printout when more than 2GB is allocated.

Modeller 9.13 release 02-12-2014:
  - Modeller now includes a variety of SOAP (statistically optimized atomic
    potential) scores for assessing proteins, loops, and interfaces.
  - Bundled version of HDF5 updated to 1.8.10.
  - The Lennard-Jones interaction energy is now artificially truncated at
    very short distance; this makes simulations with poor starting conditions
    much less likely to 'blow up'.
  - Residue, Atom and Chain objects can now be meaningfully compared in Python
    (previously == would always return False).
  - model.get_insertions(), model.get_deletions() and model.loops() now have an
    include_termini option; if False, residue ranges that include chain termini
    are excluded from the output.
  - Most Modeller objects can now be written to or read from file handles
    (e.g. modfile.File(), or any Python filelike object) as well as named
    files.
  - automodel now accepts file handles or alignment objects for the 'alnfile'
    parameter.
  - Structure.read() allows reading an alternative conformation of a template.
  - User-defined energy terms can now report violations and energy profiles.
  - The sigma factor for EM fitting can now be modified (density.sigma_factor).
  - Bugfix: have Restraints.make_distance() restrain distances where the
    template is a non-standard residue with a standard backbone (e.g. UNK,
    ASX, GLX).
  - Bugfix: don't falsely warn about topology being available for every
    BLK residue when automodel reads the initial model PDB file back in.
  - Bugfix: model.get_insertions() previously ommitted the first residue
    of insertions in some cases, while model.get_deletions() incorrectly
    handled overhangs and a single residue between two deletions.
  - Bugfix: model.build() no longer crashes when trying to interpolate and
    exactly one atom in the segment has defined coordinates.
  - Bugfix: model.build() no longer uses atoms in a different chain
    as anchors for interpolation.
  - Bugfix: derivatives of the angle feature are now more stable when the
    angle is close to 180 degrees.

Modeller 9.12 release 06-12-2013:
  - Modeller is now only supported on Mac OS X 10.6 or later.
    If you want to run Modeller on older OS X releases, use Modeller 9.11.
  - alignment.align(), alignment.salign() and alignment.align2d() now attempt
    to keep chain breaks aligned when aligning multi-chain sequences.
    This behavior can be tuned with the break_break_bonus parameter.
  - alignment.edit() has a new by_chain parameter; if set, overhangs are
    removed for each chain in multi-chain alignments.
  - alignment.edit() now returns the number of residues that it removed.
  - Align codes (identifiers of sequences in alignment objects) can now be of
    any length. (Codes in profile and sequence_db objects are still limited to
    40 characters.)
  - model.build() now does a better job of generating coordinates starting
    from just CA positions.
  - generate.transfer_xyz() now generates better structures for 6-membered
    rings. (Previously, initial models could occasionally contain such badly
    distorted rings that the optimizer was not able to recover the correct
    geometry in the final models.)
  - Atoms in BLK residues are now assumed to have typical heavy-atom radii
    when calculating Lennard-Jones interactions, similar to soft-sphere
    (previously no interaction was calculated).
  - Atom types can now be changed by assigning to Atom.type. This can be
    useful when employing BLK residues to use more accurate radii.
  - A new function automodel.guess_atom_types() can now be called to try to
    assign more appropriate atom types for BLK residues.
  - Modeller now matches residues in PDB files using both name and ATOM/HETATM
    indicator; previously just the name was used. This allows for correctly
    reading PDB files containing amino acid ligands, for example (they were
    previously forcibly mapped to ATOM on output).
  - Added support for Python 3.3.
  - Bundled version of HDF5 updated to 1.8.9.
  - Bugfix: Q* and UNK atoms are no longer silently skipped when reading PDB
    files.
  - Bugfix: don't weaken distance basis restraints too much when two means are
    too far apart, since this can cause a numeric overflow in
    Restraints.spline() later.

Modeller 9.11 release 09-06-2012:
  - sequence_db objects now only store part of the sequence database in memory
    when using a binary (HDF5) file (databases in PIR or FASTA format still
    must be read in in their entirety). Functions that use sequence databases
    now take a 'window_size' argument, that controls how much of the database
    is read into memory at one time. This results in much lower memory usage
    when using large databases such as UniProt.
  - Limits on the numbers of atoms and bonds per residue have been removed.
  - SSBOND and CONECT records are now written to PDB files when models
    containing disulfides are saved.
  - The default behavior of automatically converting common modified residues
    (MSE, MEX, ABU) to their standard equivalents can now be disabled by
    setting env.io.convert_modres=False.
  - Rather than silently truncating align codes to the internal maximum
    length (of 40 characters), too-long codes now result in an error.
  - alignment.get_suboptimals() now takes an align_block argument to support
    suboptimal alignments of two previously-aligned blocks of sequences.
  - Bundled version of HDF5 updated to 1.8.8.
  - Bugfix: Chain.join() now works correctly when joining adjacent chains.
  - Bugfix: when converting MSE residues to MET, set the element correctly
    for the SD atom (to S; previously it was left as SE).
  - Bugfix: improve matching of alignment sequence to PDB when using '.'
    in the alignment header and PDB contains duplicate residue numbers.
  - Bugfix: parallel loopmodel runs no longer leak memory.
  - Bugfix: alignment.salign() no longer leaks memory on encountering an
    error.
  - Bugfix: on machines without networking, allow parallel runs with
    local_slaves only (rather than failing to create a job object at all).

Modeller 9.10 release 09-28-2011:
  - Add Python 3 support.
  - Add support for Mac OS X 10.7 (Lion).
  - Modeller on 64-bit Macs is now built with Intel Fortran, resulting in
    a roughly 2x speedup compared to 9.9.
  - Add Unicode support; all filenames should be UTF-8 encoded.
  - CHARMM angle restraint on GLN OE1 and ASN OD1 atoms strengthened to
    avoid generating poor stereochemistry for these residues.
  - Bugfix: atoms with undefined coordinates are assigned zero accessibility.
  - Bugfix: selection.superpose() no longer fails if given residues containing
    multiple selected atoms with the same name.
  - Bugfix: don't create empty .DLxxx files when loop modeling with
    automodel.trace_output set to 0.
  - Bugfix: model.to_iupac() now correctly handles hydrogen atoms in
    Arg residues.
  - Bugfix: fix a crash in alignment.write() with certain large alignments.
  - Bugfix: set model.seq_id correctly when using a user-supplied initial
    model with automodel.
  - Bugfix: don't force HSE and HSP residues to be ATOM; leave them as HETATM
    if they are so labeled in the input PDB.

Modeller 9.9 release 04-04-2011:
  - Modeller is now only supported on Windows XP Service Pack 2 or later.
    If you want to run Modeller on Windows ME, 2000, or NT, use Modeller 9v8.
  - Added support for Python 2.7; Python 2.5 is now supported on all
    platforms.
  - Bundled version of HDF5 updated to 1.8.5-patch1.
  - Initial models generated by automodel now always contain valid PDB
    coordinates, i.e. each coordinate is in the range -999.999 to 9999.999.
  - During loop modeling, if atoms are missing from the initial model,
    loopmodel.loop.write_defined_only can be set True to write out PDBs
    containing only non-loop atoms present in the initial model.
  - Restraints using user-defined one-dimensional mathematical forms can now
    be converted to splines using Restraints.spline().
  - Bonds between protein atoms and BLK residues are now restrained more
    strongly than regular BLK-Calpha distances.
  - alignment.salign() now generates the requested number of suboptimal
    alignments, not one less.
  - When reading new-style PDB files (with element names in columns 77-78)
    Modeller will now use this information to determine whether an atom is a
    hydrogen. (With old-style or non-conformant PDB files, it will continue to
    guess based on the atom name, so will not read mercury ions for example
    unless env.io.hydrogen=True, since it cannot unambiguously determine
    whether HG is mercury or "hydrogen bonded to CG".)
  - The Windows installer now supports silent installation with the /S flag.
    Use the /D flag to specify install location and /KEY to specify the Modeller
    license key, e.g. setup.exe /S /KEY=xxx /D=C:\Program Files\modeller
  - Bugfix: complete_pdb() now preserves chain IDs.
  - Bugfix: environ.dendrogram() no longer crashes if given a distance
    matrix of size zero.
  - Bugfix: Random seed is no longer ignored by model.make_region().
  - Bugfix: MET residues marked as HETATM (e.g. ligands) are now correctly
    skipped when env.io.hetatm=False (previously they were read in).
  - Bugfix: lookup of atoms by name in models containing duplicated
    residue and/or chain names now works correctly.
  - Bugfix: fix PSA crash on models containing no amino acids.
  - Bugfix: alignment.get_suboptimals() no longer fails to parse alignments
    where neither sequence starts at the N terminus, and now correctly handles
    alignments where the C termini are misaligned.
  - Bugfix: sequences in PAP files can now start in any column (as long as
    all the sequences start in the same column), not just column 11.
  - Bugfix: allow atom names in the group_restraints atom class file to
    contain single-quote characters (e.g. nucleic acid atoms such as O3').
  - Bugfix: fix range of spline math forms when resplined by
    Restraints.spline().

Modeller 9v8 release 04-26-2010:
  - Residues treated as BLK no longer have to be HETATM residues; they will
    be marked as ATOM if so defined in restyp.lib or in the template PDB
    (for example, DNA or RNA residues). automodel.nonstd_restraints() now
    builds restraints on both HETATM and BLK residues.
  - Python methods that previously expected lists or tuples can now work with
    other iterables too (such as generators). For example, in Python 2.4 you
    can now say 's = selection(x for x in mdl.atoms where x.biso > 0.5)' to
    select all atoms with Biso over 0.5.
  - The file argument to model.write_data() is now optional, since we may only
    want the calculated property in Biso, and some properties (e.g. CRV)
    cannot be written to files anyway.
  - Models read with model.read() or complete_pdb() now have model.rfactor
    set from the relevant PDB records.
  - Bonds between BLK residues are now detected by a simple distance criterion
    and are restrained more strongly than other distances by
    automodel.nonstd_restraints().
  - A new method Chain.join() allows chain breaks between chains to be removed.
  - Files compressed with xz can now be read, provided that the xz binary
    is available on your system.
  - Bundled version of HDF5 updated to 1.8.3.
  - The allow_alternates option to alignment.append() will now allow G in the
    alignment sequence to match any non-standard residue type in the PDB file
    which maps to G. This is useful if the alignment sequence is 'cleaned' as
    by sequence_db.read().
  - When using GB/SA with BLK residues, each BLK atom will now be treated as
    an uncharged particle with a small radius, rather than causing an error.
  - In sequence_db.filter(), if two sequences fail to align, don't terminate
    the entire run; rather, place them in separate clusters.
  - density.read() now supports CCP4 files, and reads the map and voxel sizes
    from the density map file header if not specified by the user.
  - Bugfix: invalid PAP files no longer crash Modeller with an assertion
    failure.
  - Bugfix: projected coordinates from environ.principal_components() are
    now written correctly to the output file.
  - Bugfix: models can now be built containing HSE or HSP residues without
    the program terminating with a cryptic MDT error; homology-derived
    restraints for these residues will look very similar to those for HIS.
  - Bugfix: assigning to Residue.num now gives a correctly-formatted
    (right-aligned) PDB residue number by default.
  - Bugfix: assigning to r.type, r.code, r.name or r.pdb_name, where r is a
    residue in an alignment, now works correctly (previously, the new
    one-letter code was not used when the alignment was written to disk).
  - Bugfix: mainchain curvature values for terminal residues were incorrect
    in some cases.
  - Bugfix: mainchain curvature calculation no longer spans chain breaks.
  - Bugfix: in profile.scan(), if the target profile has no name, do not
    trigger a GLib CRITICAL error.
  - Bugfix: automodel with write_intermediates=True now works correctly.

Modeller 9v7 release 06-16-2009:
  - A new method alignment.get_suboptimals() allows the suboptimal alignment
    file generated by alignment.salign() to be easily parsed.
  - A new method iterative_structural_align() provides a
    straightforward way to obtain the best SALIGN structure-structure alignment.
  - Problems with statistics (e.g. profile.build() on a small database) now
    raise a StatisticsError rather than the more generic ModellerError.
  - Sequence mismatches between PDB files and alignments now raise a
    SequenceMismatchError rather than the more generic ModellerError.
  - alignment.append() and alignment.read_one() now take a new argument,
    allow_alternates, which allow for alternate matches of one-letter codes
    when reading PIR sequence ranges from PDB files (B to N, Z to Q).
  - An error message is now reported when using an alignment containing an
    empty sequence, and reading of the full sequence from a PDB file fails.
  - Tab characters in alignment files are now treated the same as any other
    whitespace, and do not result in cryptic failures.
  - Parallel jobs have a new method, job.yield_tasks_unordered(), which is
    like job.run_all_tasks() but which returns results as they are generated
    rather than when all the tasks have finished.
  - Parallel jobs now default to trying to duplicate the current Python
    environment (using modslave.py and modpy.sh if necessary) when setting
    "modeller_path", rather than running the mod9v7 script, since the latter
    may conflict with the Python version of the master.
  - Bugfix: TER records are now emitted even for single chain proteins,
    and contain a unique serial number, the correctly formatted residue name,
    and the chain ID, as per PDB specifications.
  - Bugfix: correct slave Python search path when a parallel job master
    script is run from a directory other than the current working directory.
  - Bugfix: profile.build() no longer crashes when searching empty or very
    small (less than 10 sequences) sequence databases.
  - Bugfix: density.grid_search() no longer exhausts the stack when using
    large density maps.
  - Bugfix: PROFILE or BLOCK alignment with alignment.salign() should now work
    correctly even when align_block=1.
  - Bugfix: alignment.malign() and alignment.salign() now work correctly
    with alignments containing zero-length sequences.
  - Bugfix: when reading multiple copies of the same align code from an
    alignment file, all sequence metadata is now duplicated correctly.
  - Bugfix: scores from the multiple binormal restraint were slightly
    incorrect in some cases.
  - Bugfix: initial loop models containing hydrogens are now read back in
    correctly (fixes an 'Index x out of range' error).
  - Bugfix: residues marked in PDB file REMARKs as BLK are preserved as
    BLK (rigid bodies) when the PDB is read back in, even when their name
    appears in the topology library.
  - Bugfix: PDB RESOLUTION lines should now be parsed correctly in both
    old-style (v3.1 or older) PDB files and new-style (v3.2) PDBs.

Modeller 9v6 release 02-09-2009:
  - Added support for Python 2.6.
  - Use 64-bit integers for indexes to residues in sequence databases, to
    allow databases containing more than 2 billion residues.
  - Bugfix: compressed files now work correctly on Windows (no more
    "Bad file descriptor" errors).
  - Bugfix: add some bonds that were missing from the DADE, GDP and NAD
    topologies.
  - Bugfix: correction of a minor inaccuracy in the SAXS excluded volume
    calculation.
  - Bugfix: profile.build() no longer exhausts the stack when scanning against
    very large databases (e.g. UniProt).
  - Bugfix: allow running more than 99 steps of EM grid search.
  - Bugfix: output MRC files now contain the correct cell and voxel size.

Modeller 9v5 release 10-16-2008:
  - Default gap_penalties_1d for alignment.align2d() have been changed to match
    the optimized 2D penalties, as determined from a test alignment set.
  - automodel now constrains any protein-ligand close contacts (less than 2.3A)
    to attempt to preserve protein-ligand chemical bonds.
  - New normalized DOPE assessment method, which returns a Z-score, and is thus
    comparable between different proteins (see model.assess_normalized_dope()).
  - Bundled version of HDF5 updated to 1.8.1.
  - PDB atom files are now also looked for in PDB-style subdirectories (the
    first two characters after the digit); e.g. 1abc is searched for in the
    'ab' subdirectory, pdb4xyz.ent in the 'xy' subdirectory.
  - Libraries updated to correctly read and write remediated RNA and DNA,
    some other HETATMs (e.g. ions) and to use the new hydrogen names, in PDB v3.
  - Modeller now outputs new-style PDBs, with the element in columns 77 and 78,
    rather than older-style PDB which has a sequence number in this position.
  - Enable Large File Support, to correctly read files bigger than 2GB on
    32-bit Unix systems.
  - Remove unused residue_grouping and distance_atoms arguments from
    Restraints.make().
  - Bugfix: no longer ignore excluded pairs between two BLK residues.
  - Bugfix: selection.only_mainchain() now considers OXT atoms to be mainchain.
  - Bugfix: alignment.append_model() no longer crashes when trying to add a
    structure containing only one atom.
  - Bugfix: Topology.make() should now preserve complete IC/BILD entries for
    patch residues.

Modeller 9v4 release 05-15-2008:
  - The speed of GB/SA calculations has been dramatically increased; the
    cutoff distance used in the GB/SA calculation can also now be adjusted to
    balance speed against accuracy (the default cutoff has been decreased from
    15.0A to 8.0A).
  - alignment.append() no longer takes rewind_file and close_file arguments;
    they did not work correctly anyway. New method alignment.read_one() added
    to read sequences one by one from a PIR or FASTA file.
  - alignment.write(), model.write(), selection.write(), Chain.write() and
    Structure.write() now take either a file name or a file handle
    (modfile.File()).
  - Split alignment.check() into alignment.check_structure_structure() and
    alignment.check_sequence_structure(). Both functions now return the number
    of pairs which exceeded the cutoffs, which are also adjustable.
  - alignment.compare_with() now returns the percentage of equivalent
    residue-residue pairs in the two alignments.
  - 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 (${MODELLER_TMPDIR}
    if set, otherwise the system temporary directory if possible, otherwise the
    current working directory). 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.
  - Files compressed with p7zip can now be read, provided that the 7za binary
    is available on your system. Such files should contain only a single member
    (e.g. a file foo.pdb could be compressed into the archive foo.pdb.7z).
  - Update PDB files used in the examples (remediated PDBs are now used).
  - Added selection.only_water_residues() method, which selects only atoms in
    water residues.
  - User-defined energy terms now take a cutoff parameter to use the
    non-bonded list.
  - Bugfix: use the basename, not the full path name, to generate output file
    names in density.grid_search().
  - Bugfix: model.transfer_xyz() with cluster_cut > 0.0 incorrectly calculated
    the number of atoms in each residue, which in some circumstances could
    cause a crash.
  - Bugfix: miscellaneous alignment.salign() fixes.
  - Bugfix: alignment.append_model() now copies the model's resolution,
    R-factor, name and source to the alignment.
  - Bugfix: if two or more different types for a single residue are listed in
    a PDB with alternate location codes (e.g. 80:A in 1en2), only the first
    is read by Modeller.

Modeller 9v3 release 02-05-2008:
  - Mac OS X 10.5 (Leopard) is now supported (with Python 2.5).
  - Added structure.write() method, to write out current template
    structures as PDB files.
  - Added chain.write(), chain.filter(), and chain.atom_file_and_code()
    methods, to write out sequences of individual chains. These obsolete the
    model.make_chains() method.
  - Added selection.only_defined() method, which selects only atoms with
    defined coordinates.
  - The GB/SA scorer is now implemented as a user-defined energy term;
    energy_data.dynamic_gbsa has thus been removed.
  - User-defined energy terms in C now get passed additional libraries and
    energy_data parameters.
  - Invalid headers in PIR alignment files now result in an error, to avoid
    potential problems with these headers going unnoticed.
  - File format errors now have their own Python exception - FileFormatError -
    which is a subclass of the generic ModellerError.
  - alignment.align() and alignment.consensus() no longer take a
    max_gap_length parameter, as it is not used in any case.
  - Profile objects now have a positions member, which is a list of all
    aligned positions, similar to the same member for alignment objects.
  - selection.debug_function() now returns the number of derivatives which
    exceeded the cutoffs.
  - Bundled version of HDF5 updated to 1.6.6.
  - Bugfix: always read the first PDB alternate location encountered for each
    residue, not only A or 1, which resulted in skipping of residues which
    used neither of these codes.
  - Bugfix: no longer limit atom file names in PIR comment lines to 80
    characters.
  - Bugfix: user-defined mathematical forms no longer cause an error in
    restraints.pick() when restraints_filter is not -999.
  - Bugfix: the scoring function will return an error if a coordinate has
    become infinite or not-a-number (e.g. due to a bad optimization).
  - Bugfix: the INITIAL_MALIGN3D option works again with TOP scripts.
  - Bugfix: selection.superpose() now returns correct values for num_equiv_pos
    and num_equiv_dist (previously these were erroneously the same as the
    cutoff values).
  - Bugfix: calling selection.energy() from within an optimizer periodic
    action no longer causes the optimization to cycle endlessly.
  - Bugfix: alignment.append_model() now puts the current model coordinates
    into the alignment, not the PDB in its original orientation.

Modeller 9v2 release 08-08-2007:
  - Added loopmodel.user_after_single_loop_model() method.
  - Added loopmodel.loop.library_schedule and loopmodel.loop.max_var_iterations
    members, to allow the loop modeling optimization protocol to be modified.
  - 'parallel' module should now work on all platforms, provided Python is
    available.
  - sge_qsub_job() now groups all automatically-spawned qsub jobs into SGE
    task arrays.
  - dope_loopmodel's confusingly-named initial_model argument is now removed.
    To provide an initial loop conformation, override the
    loopmodel.build_ini_loop() method.
  - By default, automodel now only randomizes starting coordinates for
    residues with defined topology (previously it also randomized BLK
    residues, and in some cases the optimizer was then unable to recover their
    rigidity). To override this behavior, set automodel.rand_method.
  - alignment.salign() now takes a 'rms_cutoff' argument with a single RMS
    value, rather than an 11-element 'rms_cutoffs' list, since only the first
    value from this list was used, and alignment.compare_structures() now takes
    a single 'varatom' argument rather than a 2-element 'distance_atoms' list,
    for the same reason.
  - All relevant data (initial RMS plus cutoff values) are now returned from
    selection.superpose().
  - The API has been cleaned up and given a much more logical structure.
  - Windows and Linux installs of Modeller now support Python 2.5. (On other
    platforms you can recompile the Python interface yourself for 2.5.)
  - The scaling of rigid body angles in CG and QN optimizations can now be
    tuned. The restraints file format for rigid bodies has changed accordingly.
  - Switch from CHARMM to PDB naming for atoms in nucleic acids. DNA/RNA can
    now be used by default in alignments by using the a, c, g, t and u
    one-letter codes.
  - Some of the alignment and profile functions have had redundant arguments
    removed (e.g. profile.scan() no longer takes a write_summary argument, as
    this is defined by the value of the summary_file argument).
  - restraints.spline() now takes Python form, feature and group objects rather
    than numeric 'spline_select' values.
  - The default value of automodel.max_molpdf has been increased from 1e5 to
    1e7, since some larger systems can legitimately exceed the smaller value.
  - Bugfix: BLK residues written out in PDB files (e.g. in initial models) are
    now correctly read back in as BLK residues, even if they have the same
    name as a non-BLK residue type.
  - Bugfix: in some cases, dihedral restraints were acting on the wrong atoms
    after the user called model.patch().
  - Bugfix: do not build dihedral restraints (phi/psi, omega) between residues
    in different chains.
  - Bugfix: remember template coordinates, so that automodel.initial_malign3d
    works correctly and gives reasonable initial models.
  - Bugfix: suboptimal alignments are now written to the
    suboptimal_alignments.out file, not to the log file.
  - Bugfix: opening the same gzipped file simultaneously from two separate
    Modeller processes should now work correctly.
  - Bugfix: conflicting omega restraints are now correctly removed from
    systems containing ligands, even if they are not at the end of the sequence.
  - Bugfix: patches that act on two residues (e.g. DISU) can now correctly add
    or remove atoms that have names longer than 2 characters.

Modeller 9v1 release 01-22-2007:
  - Initial models (inifile argument to automodel()) are now handled more
    robustly. They must have the same amino acid sequence as the template,
    but missing or misordered atoms will be added/reordered automatically.
  - 'add_segment' argument removed from model.generate_topology(). Call
    model.clear_topology() first if you want to initiate the model.
  - model.write_pdb_xref() command removed. Residue objects provide all
    necessary information.
  - 'selection_mode' and 'extend_hot_spot' arguments removed from
    selection.hot_atoms(). Use selection.extend_by_residue() instead.
  - 'model.rotate()' command removed. Use selection.translate(),
    selection.transform(), or selection.rotate_origin() instead.

Modeller 9v0 release to Accelrys: 09-05-2006:
  - A new more sensitive assessment method is provided, high resolution DOPE;
    see selection.assess_dopehr().
  - A new loop modeling protocol, relying on the DOPE method, can be used to
    obtain higher quality models in many cases, at the expense of more CPU time.
    See the dope_loopmodel and dopehr_loopmodel classes.
  - The speed of profile searches is now dramatically increased by storing the
    template profiles in a PSSM database. See profile.scan().
  - Profile commands now handle non-standard residues, which are treated as
    equivalent standard residues (as defined in restyp.lib). Consequently, the
    'clean_sequences' argument to alignment.to_profile() has been removed.
  - Allow the number of PDB residues to be specified unambiguously in PIR files
    (correctly handling the case where PDBs contain duplicated residue numbers).
  - Universal binaries provided for Mac (i.e. both Intel and PPC Mac OS X).
  - model_segment will no longer read file names and residue ranges from an
    alignment; use the alignment object directly if you need access to this
    information for model.read().
  - Generated models with multiple chains now have these chains labeled A, B, C,
    and so on. A chain break in a model is now taken to correspond to a change
    in chain IDs in a PDB file (previous versions used the TER records). If
    building models with ligands, you may need to move your alignment chain
    breaks from before to after the ligands, to get the correct final chain IDs.
  - The pdbent.lib file, which maps PDB codes to filenames, is no longer used.
    If your PDB file names are not in a standard form (e.g. pdbxxxx.ent or
    xxxx.pdb) then you can give Modeller explicit filenames. If you were not
    using the pdbent.lib file before, you will not be affected by this change.
  - The new sequence_db.convert() command converts sequence databases to
    binary format sequence-by-sequence, and so uses much less memory than
    sequence_db.read() followed by sequence_db.write().
  - USER restraints format is no longer supported.
  - The CHAINS_* files in the modlib directory, containing all PDB sequences
    filtered by sequence identity, have been removed. You can download up to
    date versions of these files from the Modeller download page, or build
    them yourself using a local copy of the PDB and sequence_db.filter().
  - model.optimize() has been replaced with two optimizer classes;
    conjugate_gradients() and molecular_dynamics(). The trace_output variable
    and model.switch_trace() command have also been replaced, with
    actions.trace(). There is also a new state_optimizer() class, for building
    your own optimizers, and a quasi_newton() class, for quasi-Newton
    (variable metric) minimization.
  - The molecular_dynamics() optimizer now supports self-guided MD, for
    improved sampling.
  - The old implicit schedules have been removed; if you wish to use an
    optimization schedule, you must use an explicit schedule() object.
    automodel's library_schedule variable now takes such an object, rather
    than a number between 1 and 7.
  - The old 'picked atom sets' 1 through 3 have been replaced with a new
    selection object. Selections allow arbitary atoms or atom groups to be
    added or removed, and support standard mathematical set operations.
    * The following commands now act on selection rather than model objects:
      selection.mutate(), selection.randomize_xyz(), selection.superpose(),
      selection.rotate_dihedrals(), optimizers, selection.energy(),
      selection.assess_dope(), selection.debug_function(), selection.unbuild(),
      selection.hot_atoms().
    * The 'pick_atoms' command has thus been removed.
    * If you redefine the 'select_atoms' or 'select_loop_atoms' methods in
      automodel or loopmodel, note that these should now return a selection
      object. Some other automodel/loopmodel methods now take selection rather
      than model objects, such as loopmodel.build_ini_loop(), and all of the
      generate and refine methods.
    * Rather than restraints.make(), use restraints.make_distance() for
      DISTANCE and USER_DISTANCE restraints, and the secondary_structure
      module for ALPHA, STRAND and SHEET restraints.
    * The following commands now take a single selection object argument:
      restraints.pick(), restraints.make()
    * The following command now takes two selection object arguments:
      restraints.make_distance()
  - Default gap_penalties_2d have been changed; the new defaults were found to
    be optimal for a test alignment set (see alignment.align2d()).
  - Binary files are now read or written in industry-standard HDF5 format,
    and are now machine-independent. Their contents can be inspected with
    any program which understands the HDF5 format. Note, however, that they
    are not compatible with old versions of MODELLER (you will have to
    regenerate any old binary files from their text equivalents). See
    sequence_db.read(), sequence_db.write(), profile.read() and profile.write().
  - EM densities can now be read or written in MRC format as well as XPLOR.
  - Warn, rather than crash, if a restraints file with negative or zero
    atom indices is read.
  - Restraint forms, groups, and features are now specified with Python
    objects, and new forms and features can be implemented by the user in
    Python or C. Consequently, 'USER_DISTANCE' restraints have been removed.
  - Symmetry restraints are now also specified with Python objects; the
    symmetry.define() command has been removed.
  - restraints.unpick() now takes one or more Python atom objects, rather than
    atom names.
  - On most platforms, Modeller is now distributed as a shared library by
    default, allowing it to be used like an ordinary Python module, or to
    be linked against other programs.

Modeller 8v2 release 02-28-2006:
  - Bug fix for model_segment: specifying 'FIRST:@', 'LAST:' will now read in
    all chains in a multi-chain PDB, even when the first has no ID.
  - Bug fix: chain breaks were sometimes being placed incorrectly in
    written-out alignments.
  - Bug fix: some Python circular references, which were preventing memory
    from being freed, have been removed, thus fixing some long-running scripts.
  - Bug fix: pseudo atom tables are now reset where necessary; fixes some
    'atom index out of range' errors.
  - Bug fix: local alignments with alignment.salign() were incorrect in some
    cases.
  - Bug fix: alignment.compare_structures() was calculating incorrect RMS
    values in some cases.
  - New optimized 2D gap penalties are now used for alignment.salign() by
    default.
  - More explanatory error messages for the common 'mismatch between
    alignment and PDB' problem.
  - The number of segments for DRMS computation (nsegm) and the matrix offset
    for structural local alignment (matrix_offset_3d) can now be specified
    in alignment.salign().

Modeller 8v1 release 06-20-2005:
  - 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 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 restraints.pick() when used with absolute position restraints;
    always allow 1-atom restraints to pass the residue_span_range check.

Modeller 8v0 release 04-14-2005:
  - Switch from TOP to Python as the primary scripting language.
  - Incorporation of the GA341 and DOPE methods for model assessment.
  - Improved handling of dynamic memory, and removal of various limits such
    as MAXRES.
  - New alignment.salign() alignment, based on the COMPARER program.
  - Various fixes to profile.build(), and a new profile.scan() command.
  - density.grid_search() allows docking of models to EM density maps.
  - Modeller will now read compressed files in the .gz and .bz2 formats
    (as well as the existing .Z format) provided the gzip and bzip2
    programs are available.
  - Fix for various problems reading alignment files with very long lines,
    or with Mac, Unix or DOS-style line endings.
  - Bug fix for alignment.compare_structures(); disulfide bridges were not
    being properly considered in the comparison.
  - Bug fix: atom names in which the first character does not match the
    element (e.g. in NAD, where they begin with A or N) should now be
    correctly aligned in output PDB files.
  - Charges for all topologies are now assigned using a `nearest neighbor'
    technique in topology.make().

Modeller 7v7 release: 09-15-2004
  - New features allow restraining absolute atomic positions and differences
    between two dihedral angles.
  - Point-and-click Windows installer, and Mac OS X 10.3 support.
  - Basic support for mmCIF files
  - Bug fix for beta (strand) restraints
  - SALIGN, PROFILE_PROFILE_SCAN, and EM_GRID_SEARCH commands are disabled
    for this release (still under development)

Modeller 7v0 release to Accelrys: 01-31-2003
  - 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.
  - CHARMM topology libraries are now PDB (IUPAC) compliant, i.e.
      HSD -> HIS
      ILE CD -> ILE CD1
      LEU CD1 -> LEU CD2
      LEU CD2 -> LEU CD1
    PDB hydrogen naming conventions apply.
    See modlib/top-charmmH.lib for old CHARMM-style naming, and comments
    at the start of modlib/top.lib.
  - READ_ALIGNMENT can now read FASTA format. When reading PIR or FASTA
    alignments, the CLOSE_FILE, REWIND_FILE and END_OF_FILE variables are
    checked; such files will be left open if CLOSE_FILE is zero so that
    future reads will start partway through the file, provided REWIND_FILE
    is zero. END_OF_FILE is set to 1 if READ_ALIGNMENT reached the end of
    the file.
  - Initial code for 2D spline restraints.
  - New 'CAV' output option for WRITE_DATA, which writes out protein and
    internal cavity volumes (not currently functional).
  - MALIGN3D uses the EDIT_FILE_EXT variable to allow customization of the
    _fit extension for fitted atom files.
  - 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, PROFILE_PROFILE_SCAN
  - Alterations to variable gap penalty for dealing with profiles (new WsC
    parameter to GAP_PENALTIES_2D).
  - 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'.
  - New TIME_MARK command for benchmarking.
  - New 'SALIGN' alignment, using structural information, and based on the
    COMPARER program.
  - Other new commands: SEQFILTER, MAKE_CHAINS, VOLUME, VOLUME_CAVITY.

Modeller 6v2 release: 05-14-2002
  - MODELLER has been ported for the Apple Mac OS X operating system.
  - Dynamic memory allocation algorithm, which should increase the
    stability of MODELLER
  - IBM executable for AIX OS added
  - Windows version of MODELLER 6v2!* For time being it is distributed as
    a separate executable, although we plan to incorporate it with the rest
    of the package.
  - Big change is made with respect to the MODEL_SEGMENT. The residue number
    for the first position (res_ID1) in the MODEL_SEGMENT
    range (res_ID1:chain_ID1 res_ID2:chain_ID2) can be either a real residue
    number or 'FIRST' (which indicates the first residue in a matching chain).
    The residue number for the second position (res_ID2) in the MODEL_SEGMENT
    range can be either: a real residue number; 'LAST' (which indicates the
    last residue in a matching chain); or 'END' (which indicates the last
    residue in the PDB file). The chain id for either position in the
    MODEL_SEGMENT range (chain_ID1 or chian_ID2) can be either: a real chain
    id (including a blank/space/null/empty); or '@', which matches any chain
    id. Examples, assuming a two chain PDB file (chains 1 and 2):
    'FIRST:@ 10:@' reads residues 1 to 10 in chain 1; 'FIRST:@ LAST:@' reads
    all residues in chain 1, assuming 'FIRST' is not a real number of the
    non-first residue in chain 1 (similarly for the LAST); '10:@ LAST:' reads
    all residues from 10 in chain 1 to the end of the file (chain id for the
    last residue is irrelevant), again assuming 'LAST' is not a real residue
    number of a non-last residue; 'FIRST:@ END:' reads the whole file no
    matter what, the chain_ID is ignored completely. For the SELECTION_SEGMENT
    the string containing `@' will match any residue number and chain_ID.
    For example, `@:A' is the first residue in chain `A' and `@:@' is the
    first residue in the coordinate file. The last chain can not be specified
    generically, except for the last residue in the file.

Modeller 6v1 release: 01-25-2002
  - ALIGN2D: Corrected weighing of the gap spanning distance term and
    calculating the average gap spanning distance for multiple templates.
  - READ_MODEL: Retained atomic charges of a model even after READ_MODEL
    from a PDB file (allows the use of the Coloumb terms with the __model
    script). Charges were zero before.
  - READ_RESTRAINTS: Corrected reading of restraints from a file in the
    USER format. No restraints were read before.
  - MAKE_SS_TEMPLATES: Corrected automatic imposition of disulfides on the
    target, from aligned templates. No disulfides were imposed before.
  - __model script: The original alignment file is not overwritten by the
    modeling alignment anymore. In 6v0, it was.
  - Executable for Mandrake implementation of Linux added.

Modeller 6v0 release: 12-26-2001
  - Dynamic memory allocation removed limits on the size of most arrays,
    including model and alignment arrays.
  - The new TOP loop modeling routine 'loop' significantly improves the
    accuracy of loop modeling. It can also be used in modeling of sidechains
    or any other parts of the structure.
  - A statistical atomic distance-dependent potential can be used for
    modeling and model evaluation.
  - The new ENERGY OUTPUT = 'ENERGY_PROFILE' command allows construction
    of energy profiles for model evaluation, based on any combination of
    MODELLER energy terms. It replaces the ENERGY_PROFILE command.
  - New functional form and parameters for the binormal (Phi, Psi) restraints
    improve their numerical stability and accuracy.
  - New TOP command SEGMENT_MATCHING facilitates exploring many different
    alignments in the difficult comparative modeling cases.
  - Many bugs fixed, many small changes and improvements made.
  - Redesigned MODELLER web site.

01-01-2000:
  - AŠ: too numerous changes to list here, conversion from f77 to f90.

09-15-1998:
  - AŠ: changed default NONBONDED_SEL_ATOMS from 2 to 1, in top.ini.

09-10-1998:
  - AŠ: updated COMPARE_SEQUENCES so that variability of the first sequence
    in the alignment is written to the Biso column of MODEL.

08-24-1998:
  - AŠ: introduced NO_TER.
  - AŠ: made a vector out of RENUMBER_SEGMENTS.
  - AŠ: introduced EXPAND_CONTROL to allow more control for the
    EXPAND_ALIGNMENT command.

07-24-1998:
  - AŠ: not using schedule in PICK_RESTRAINTS at all.

07-20-1998:
  - AŠ: biperiodic is now used

07-18-1998:
  - AŠ and AB: BUILD_METHOD for BUILD_MODEL can continue to be
    3D_INTERPOLATION, INTERNAL_COORDINATES, but can now also assume ONE_STICK
    and TWO_STICKS values to generate different initial structures for
    inserted atoms.
  - AB: New kind of error message is introduced: _B - to inform about bugs.
    Now used for former "Increase MAX..." and similar messages only.
    Scan_errors modified respectively.

07-09-1998:
  - AB: CA-only warning in READ_MODEL and other routines using rdpdb

07-08-1998:
  - AŠ: increased flexibility of ALIGN2D so that it needs only at least one
    structure for the first block of sequences.

07-07-1998:
  - AB: the multimple binormal restraints were debugged: 1) detection of most
    relevant phase of phi/psi angles 2) removal of the bug in calculation of
    the derivatives

07-01-1998:
  - AŠ: changed format of mnch.lib, removed class weights from this library
    because they occur in mnch?.lib.
  - AŠ: removed sdch.lib for sidechain classes 1-2 from all parts, including
    COMPARE.
  - AŠ: Removed undefined entries from top.ini. Changed the meaning of
    RENUMBER_RESIDUES so that it corresponds to the first residue index in
    renumbering.
  - AŠ: Added the missing ALIGN_ALIGNMENT top 'top.ini'.

06-06-1998:
  - AŠ: Added the single mutant modeling script.
  - AŠ: Modified the loop modeling scripts and other scripts so that robust
    loop modeling can be done automatically. There are at least 43 such
    arrays with a dozen diffrent character length.
  - AŠ: Expanded options to PICK_ATOMS by allowing for automated selection
    of loops; a special value for SELECTION_SEGMENT of 'LOOPS' '' and new
    variable GAP_EXTENSION were introduced.
  - AŠ: Removed SELECTION_STEP from MODELLER.
  - AŠ: Created new command SEGMENT_MATCHING for enumerating the alignments.

04-30-1998:
  - AB: In energy calculations, "slow" character parameters were replaced
    by "fast" integer ones.
  - AB: in 'model/build.F': all DISU stuff was deleted. atom classes are
    assigned based on the iss array, resnam does not change.

04-28-1998:
  - AŠ: added MNCH?_LIB libraries to allow for i-1,i,i+1 mainchain
    conformation restraints.

03-23-1998:
  - AŠ: changed ALIGN_CODES to ALIGN_CODES2 for READ_ALIGNMENT2.
  - found a workaround for a nasty compiler bug in mod2ali (for SGI, make
    opts) that caused naln=1.

03-12-1998:
  - AŠ: added option SIGNIF_CUTOFF to SEQUENCE_SEARCH.

03-05-1998:
  - AŠ: Changed the algorithm for calculating the mainchain curvature.
    Now using least-squares lines instead of simple Ca - Ca vectors.

02-27-1998:
  - AŠ: MNCH2_LIB moved to MNCH_LIB.

02-19-1998:
  - AŠ: corrected a bug in distdp3.inc which sometimes caused incorrect
    C-terminal overhang treatment, possibly incorrect alignment as a whole.

01-25-1998:
  - AŠ: changed default BUILD_METHOD back to INTERNAL_COORDINATES.

01-05-1998:
  - AŠ: Added keyword DIH_LIB_ONLY to MAKE_RESTRAINTS, to allow forcing the
    calculation of the ``homology-derived'' mainchain and sidechain dihedral
    angle restraints (single and binormal) from the residue type dependent
    libraries only (templates ignored).

02-06-1998:
  - AB: version5g/doc: Improved the html version of the manual. Changes in
    Makefile. latex2html was patched to properly handle the macros containing
    sectioning commands.

01-20-1998:
  - AB: version5g = merge (5f-ab, 5f-as). To use solvent accessibility:
    READ_PARAMETERS FILE = $LIB/par-32.lib

01-05-1998:
  - AŠ: A bug (causing a crash) in seqsearch.F is fixed.

01-02-1998:
  - AB: version 5f-ab: Introduced 32-nd physical restraint type and 7-th
    feature type (accessible surface in Ang^2). Libraries 'sched.lib',
    'feats.lib', and 'top.ini' are changed to reflect this. New logical
    variable DYNAMIC_ACCESS was introduced. Limitation, each time before
    you want to use the 32-nd feature in ENERGY etc., you have to calculate
    solvent accessibility by WRITE_DATA OUTPUT=PSA.

10-28-1997:
  - AB: the bug in rsr9 (tmps size) fixed. Restored output of the objective
    function to the output PDB file.

09-28-1997:
  - AB: New parameters:ASGL_2D_TYPE - controls the way 2D arrays are output
    by the ENERGY_PROFILE command. PROFILE_2D_PHYS - selects physical type
    to be presented as a 2D energy profile. NORMALIZE - selects normalization
    for ENERGY_PROFILE. ASGL_2D_OUTPUT - whether or not to write 2D output
    for ASGL. Command names changed: PATCH_DISULFIDES to PATCH_SS_MODEL.
    INHERIT_DISULFIDES - to PATCH_SS_TEMPLATES. ENERGY_PROFILE now outputs
    2D profiles. OUTPUT can contain the type of energy you output by
    ENERGY_PROFILE: ENERGY or IDEAL_ENERGY1, and NORMALIZE specifies the type
    of normalization. Removed the error in calculation of the spline
    non-bonded terms.

09-20-1997:
  - AŠ: Introduced the ALIGN_BLOCK argument for the MALIGN command.

09-16-1997:
  - AŠ: Modified protsize.cst and Makefile to allow more flexibility in
    defining the sizes of the most important arrays.

09-13-1997:
  - AŠ: Renamed TOP variable MODELLER_STATUS into ERROR_STATUS and moved
    it within the top.ini file.

09-07-1997:
  - AŠ: Initialized the 'ialn()' array for the PAP, INSIGHT, and QUANTA
    formats ('rdaln.F'). This bug may have caused some problems when a short
    protein is added to the alignment that contained a longer protein(framework)
    in its place (e.g., with READ_ALIGNMENT after MALIGN3D).

08-09-1997:
  - AŠ: Corrected a bug in 'preppdf.F' that sometimes resulted in a loss of
    explicitly excluded non-bonded pairs when these were not defined or read
    in before each call to 'preppdf.F'.
  - AŠ: Optimized speed of PICK_RESTRAINTS by using the 'picatm' array instead
    of the 'cnsin1' and 'cnsin2' functions.
  - AŠ: Optimized speed of MAKE_RESTRAINTS for non-bonded restraints by
    considering the selected atoms (set 1) instead of all atoms.
  - AŠ: Corrected a bug in MAKE_RESTRAINTS ('mkdyn.F') that resulted in an
    incorrect use of DYNAMIC_FLAG during calculation of the `static'
    non-bonded restraints.
  - AŠ: Modified the MAKE_RESTRAINTS command so that the calculation of the
    `static' non-bonded restraints now takes into account RESIDUE_SPAN_RANGE
    and RESIDUE_SPAN_SIGN.
  - AŠ: Added RESTRAINT_SEL_ATOMS and modified the MAKE_RESTRAINTS command
    so that the stereochemical, MRFP stereochemical, dihedral angle, and
    bi-dihedral angle restraints are calculated only when a sufficiently
    large number of atoms in a possible restraint are selected (set 1): For
    a given possible restraint, only when all restraint atoms or at least
    RESTRAINT_SEL_ATOMS are selected (set 1), is the restraint calculated.
    An exactly equivalent role for the `static' non-bonded restraints (and
    also for the `dynamic' non-bonded restraints calculated during OPTIMIZE)
    is played by NONBONDED_SEL_ATOMS (the new TOP variable that replaces and
    modifies the meaning of the old, deleted TOP variable DYNAMIC_FLAG).
    This now makes it possible to restrict the calculation of all new
    restraints to the selected atoms only (atom-atom distance restraints
    already depended on selected atom sets 2 and 3; secondary structure
    restraints are calculated for explicitly defined chain segments only).
  - AŠ: Renamed the DYNAMIC_FLAG variable to NONBONDED_SEL_ATOMS and modified
    its meaning in order to make it consistent with the new variable
    RESTRAINT_SEL_ATOMS. Old DYNAMIC_FLAG of 0 (default) is equal to the
    new NONBONDED_SEL_ATOMS of 2; and the old DYNAMIC_FLAG of 1 is equal
    to the new NONBONDED_SEL_ATOMS of 1. Impacts MAKE_RESTRAINTS and OPTIMIZE.
  - AŠ: Renamed the KEEP_RESTRAINTS string variable to the RESTRAINT_SEL_ATOMS
    integer variable and generalized its meaning (see below). Old
    KEEP_RESTRAINTS of ONE_ATOM (default) is equal to the new
    RESTRAINT_SEL_ATOMS of 1; and the old KEEP_RESTRAINTS of ALL_ATOMS is
    equal to the new RESTRAINT_SEL_ATOMS of 9999. Impacts MAKE_RESTRAINTS
    and PICK_RESTRAINTS.
  - AŠ: Changed the __model.top script so that the FINAL_MALIGN3D option
    works for alignments that use the . option for segment specification.

07-30-1997:
  - AŠ: Added keyword SWAP_ATOMS_IN_RES to SUPERPOSE. This allows swapping
    atoms in residues `DEFHLNQRVY' (as selected) to minimize sidechain RMS
    deviation between MODEL and MODEL2 that have exactly the same atoms in
    the same order (match.F).

07-22-1997:
  - AŠ: Added automatic recognition of the R, E, and P entries to the
    ADD_RESTRAINT command (it was impossible to add the excluded pairs and
    pseudo atom definitions before this modification).
  - AŠ: Simplification of the 'mod5' script.
  - AŠ: Added the READ_RESTYP_LIB command for reading new residue type
    definitions, and the corresponding RESTYP_LIB_FILE variable for specifying
    the library name.

07-19-1997:
  - AŠ: Added a check for sufficient overlap in MALIGN3D; not a stop, but
    a return in that case now.

07-13-1997:
  - AŠ: Added structure resolution to the code in the output pairwise
    distance matrix produced by the ID_TABLE and SEQUENCE_COMPARISON commands.
  - AŠ: Added arguments SIGNIF_CUTOFF and SEARCH_GROUP_LIST to the
    SEQUENCE_SEARCH command. All members of the groups that have SIGNIF
    larger than SIGNIF_CUTOFF[1] and are not more than SIGNIF_CUTOFF[2]
    units worse than the best hit are put into the alignment arrays.

07-11-1997:
  - AŠ: Changed the format of the representation of spline restraints in
    the .rsr files (MODELLER12 format changes to MODELLER5 format). The
    specs now contain only the y values, the derivatives are calculated on
    the fly. The same for the non-bonded MODELLER restraints in the
    parameter file. 

06-27-1997:
  - AŠ: Upgraded TRANSFER_XYZ by adding CLUSTER_METHOD, which selects how
    are the template-template comparisons done at each residue position ('RMSD'
    or 'MAXIMAL_DISTANCE') (routine trfxyz).
  - AŠ: Changed BUILD BUILD_METHOD = '3D_INTERPOLATION' so that the new
    ``line'' of atoms is a little randomized to prevent numerical problems
    with energy calculations (linear impropers, angles, etc.) (routine insxyz).

06-25-1997:
  - AŠ: Incorporated several minor code changes suggested by Andrzej Sawaryn
    to allow compilation with f90 on Ultra 2 running Solaris 2.5.1 (routine
    ran6, file 'Makefile').

06-24-1997:
  - AŠ: Corrected the bug in OPERATE which sometimes caused errors in using
    the result variable (e.g., with WRITE OBJECTS = RESULT) that has been
    defined by the user and not assigned a scalar value before the call to
    OPERATE (routine act13).

06-23-1997:
  - AŠ: Corrected the bug in OPERATE which sometimes caused errors in using
    the result variable (e.g., with WRITE OBJECTS = RESULT) that has been
    defined by the user and not assigned a scalar value before the call to
    OPERATE (routine act13).

modeller-4 release: 06-16-1997

03-20-1997:
  - Azat: src/io/report.F :  third kind of violation: PDF;
          src/main/top.ini:  TOP variable VIOL_REPORT_CUT2 for third kind
                             of violation
  - Improved the efficiency of SEQUENCE_SEARCH by optimizing I/O.
  - Using Roberto's extended significance tests in SEQUENCE_SEARCH
  - Added syntax checking before command execution.
  - Added additional restraints for MAKE_RESTAINTS RESTRAINT_TYPE = 'ALPHA'
    from a specific helix in one of myoglobins (O-O, CA-O), to supplement
    CA-CA and N-O hydrogen bonds.
  - Added the option to omit overhangs when writing out the alignment.
  - Added the option to omit beginning and ending residue numbers in the
    Pir format .ali file.
  - Corrected all errors in CHAINS* (mkchn.F, seqfilter.F). Now the chains
    are defined exclusively according to the chain id in the PDB files.
  - Changed the name of temporary file sys.tmp.file into time() so that
    several independent modeller jobs can be run in the same directory.
  - RESIDUE_SPAN_RANGE consists of two scalars now, not four (NRANG1 NRANG2).
    It now means the same thing in MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance',
    PICK_RESTRAINTS, and in dynamic non-bonded pairs calculation. In addition,
    a logical variable RESIDUE_SPAN_SIGN has been introduced. There are two
    conditions, the active one is selected by RESIDUE_SPAN_SIGN:
    a) NRANG1 <= |ires2 - ires1| <= NRANG2 when  RESIDUE_SPAN_SIGN = off
    b) NRANG1 <=  ires2 - ires1  <= NRANG2 when  RESIDUE_SPAN_SIGN = on
  - MAKE_RESTRAINTS: A distance restraint between a selected pair of atoms
    with residue indices ires1 (PICK_ATOMS set 2) and ires2 (PICK_ATOMS set 3)
    passes the span filter when (a) or (b) is satisfied, as selected by
    RESIDUE_SPAN_SIGN.
  - PICK_RESTRAINTS: A restraint that has all atom pairs satisfying
    condition (a) above is selected for the specified action.
    RESIDUE_SPAN_SIGN does not have any effect here.
  - Dynamic non-bonded pair list calculation: An atom pair that passes
    condition (a) is added to the list. RESIDUE_SPAN_SIGN does not have
    any effect here.
  - Added wrtmsg() routine for general message output and exit handling.
  - Corrected a serious bug in rdabrk() that probably sometimes caused
    not to read the appropriate PDB file to complete the alignment entries
    in getdata(), COMPARE, SUPEPOSE, MAKE_RESTRAINTS ...
  - The CG optimization is now more robust (an important source
    of inifinites has beeen eliminated).
  - I corrected a bug in the evaluation of the binormal Phi/Psi
    restraints. For a periodic two-dimensional variable, both variables
    and their correlation have to be taken into account simultaneously
    when calculating the deviation from the mean value (itself a vector
    of dimension 2). Thus, the new MPDF terms corresponding to the binormal
    Phi/Psi restraints will be generally different from the old ones. The
    bug was probably not very serious in terms of model quality because it
    resulted only in less efficient optimization of Phi/Psi, not in a
    minimization towards incorrect values of Phi/Psi.
  - Several constants have been increased to remove 'array too small'
    problems in 'genome' modeling.
  - Split deltaf() function into scalar and two dimensional versions
    to eliminate the IBM AIX xlf resolve problems.
  - Re-introduced the check for co-linear angles so that the optimizer
    does not crash anymore.
  - Introduced the output from the ORIENT_MODEL command.
  - Checking at the end of conmin() to see which of the two last
    structures has lowest energy.
  - Updated the examples/define-symmetry.top example.
  - Increased MRESTYP to 120.
  - Added SCHEDULE_SCALE argument to MAKE_SCHEDULE.
  - Added options FAST_SEARCH, FAST_SEARCH_CUTOFF and DATA_FILE to
    SEQUENCE_SEARCH.
  - Not writing atom type errors in atmcls() for HETATM.
  - Changed several constants (MAXCNS, MAXIMP) to allow for protein
    modeling close to MAXRES. Also increased atom index space in
    .rsr file output from i4 to i5 to allow for more than 9999 atoms.
  - Changed maxpos in string.F to allow MAXSEQ > 100.

03-18-1997:
  - Azat added TOP variable NORMALIZE_PROF for normalizing the energy profiles
    by the number of restraints per residue.

03-12-1997:
  - Released to MSI for QUANTA and InsightII 97.

01-10-1997:
  - Combined with Azat's 'dynamic' restraints changes -- but almost none
    of that code is in the current version.
  - Used flint and cvd to speed up and check the code.
  - Added non-bonded pairs list for all dynamic restraints. A huge amount
    of changes to the energy and reporting code had to be done.
  - Added special non-bonded restraints between defined atom type classes;
    they are specified in the 'MODELLER' block in the parameter library file.
  - Only the violated restraints are reported by ENERGY when
    OUTPUT = 'VERY_LONG' (before it was all restraints).
  - Corrected a bug that sometimes calculated lower and upper harmonic bounds
    without multiplying them by R*T (in the ENERGY output only, I think).
  - Corrected lowercase 'precision' to upper case 'PRECISION' in numbers.cst and
    head.F. The constants in the double precision version were single precision
    so far -- not certain about it!
  - Improved the efficiency of reading reals and integers and logicals from
    strings (str_r(), ...).
  - Added a check of sequences read in by READ_ALIGNMENT.
  - Roberto added the perl options.pl for processing the manual using top.ini
    source.
  - Added segment specs for MODEL2.
  - Coorected a bug that prevented writing out only selected atoms.
  - Added the ENERGY_PROFILE command and removed the output of OUTPUT='RESVIOL'
    from the ENERGY_COMMAND (now in ENERGY_PROFILE).
  - Changed VDW_STDV keyword to SPHERE_STDV, DYNAMIC_VDW keyword to
    DYNAMIC_SPHERE; VDW and VDW14 values in RESTRAINT_TYPE to SPHERE and
    SPHERE14; ELEC and ELEC14 values in RESTRAINT_TYPE to COULOMB and COULOMB14.
  - Added FIT option to ALIGN2D (for no alignment and just returning the 3D
    info').
  - Corrected rdpdbseq() in rdpir() so that rdpir reads the same sequence
    as rdarbk() and rdatm(), according to HETATM_IO, ...
  - Corrected the bug that made DO IVAR=1,2,3 do DO IVAR=123,123,1.

12-20-1996:
  - Made it compile under F90 on IRIX 6.2 (HOSTTYPE=F90).
  - Corrected many (trivial?) problems with IPT FLINT.
  - Added Roberto's upgrades to COMPARE_ALIGNMENTS.
  - Added Roberto's restraint type USER_DISTANCE (hydrophobic effect).
                                                                                
10-25-1996:
  - Added SPHERE_SEGMENT option to the PICK_ATOMS command. Usage:
    PICK_ATOMS SELECTION_SEARCH = SPHERE_SEGMENT, ;
               SELECTION_SEGMENT = '#RES1:C' '#RES2:C', ;
               SPHERE_RADIUS  = <real:1>
  - Changed the TOP scripts for 'model' so that READ_RESTRAINTS is done only
    once or twice per model.
  - Added value REPORT_PDB to the OUTPUT variable, which allows writing
    model files during optimization.
  - Added $+-number syntax expansion to the residue id for offsetting
    residue id's.
  - Introduced GAP_PENALTIES_1D (ALIGN and ALIGN2D),
    GAP_PENALTIES_2D (ALIGN2D), and GAP_PENALTIES_3D (ALIGN3D)
    to replace GAP_PENALTIES (ALIGN, ALIGN3D) and GAP_PENALTIES_3D (ALIGN2D).
  - Added automated addition of the 'pdb' prefix to atom filenames for
    easier atom file handling.
  - Added $(DEFAULT) and $(JOB) for generating default filenames.
  - Corrected a bug in PICK_RESTRAINTS (pickc()) that picked unselected
    restraints if ADD_RESTRAINTS = on (addrsr=.T.) (default).
  - Corrected a bug in local alignments (probably infrequent).
  - Corrected a bug that prevented C-terminal overhangs with similarity
    matrices (default).
  - Extended gap penalty definition in ALIGN2D and introduced MAX_GAP_LEN.
  - Added RENUMBER_RESIDUES option to RENAME_SEGMENTS command.
  - Added optional output to the ASGL file of the distribution of the minimal
    non-bonded distance for each atom.

08-26-1996:
  - Fixed a bug in patchss which caused bad dihedral definitions when a DISU
    patch was used with an all H topology model.
  - Added generic STD (standard) residue type for PICK_ATOMS.
  - Removed two bugs from COMPARE_ALIGNMENTS (counted % of correctly aligned
    incorrectly).

07-26-1996:
  - Added SCHEDULE_SCALE.
  - Fixed a bug in ALIGN2D so that all ALIGN_BLOCK structures are used
    in calculating the gap penalties (it did work for ALIGN_BLOCK=1, NSEQ=2
    before).
  - Introduced new command IUPAC_MODEL which swaps atoms for residues with
    C2 planar sidechains (Glu, Asp, Phe, Tyr, Arg), so that dihedrals
    observe IUPAC conventions. This is now done at the end of each
    model calculation in __single_model.
  - Introduced INIT_VELOCITIES for MD refinement. Used in __refine.top
  - Added TOP variable CURRENT_DIRECTORY for MALIGN3D command.
  - Added FIT variable to SUPERPOSE command.
  - 'model' script was modified so that all templates and models are MALIGN3D
    at the very end and written out to .fit files when
    FINAL_MALIGN3D = 1 (0 by default).
  - Added DENDROGRAM command.
  - Added EXPAND_ALIGNMENT command.
  - Only selected atoms are written out for WRITE_MODEL(2) in the PDB format.
  - Added WRITE_ALL_ATOMS flag to WRITE_MODEL.
  - Expanded SEQUENCE_TO_ALI, which now copies coordinates from MODEL to
    ALIGNMENT, too.
  - Added RMS and DRMS values to OUTPUT variable for the COMPARE command.

06-26-1996:
  - Heme group fix (courtesy of M. Sutcliffe) in top.lib, par.lib, radii.lib,
    radii14.lib, models.lib.

05-17-1996:
  - Added various output options to the wrpap() routine (sec.str,
    accessibility, variable gap penalties, etc.), selected by new TOP
    variable ALIGNMENT_FEATURES.
  - Added ALIGN2D routine for alignment of a sequence with structure(s) using
    variable gap penalty depending on helix, beta, accessibility, mainchain
    curvature, and distance between the two Calphas spanning the gap.
    Using new routines align9 and 10, and TOP variable GAP_PENALTIES_3D.
  - Added variable BUILD_METHOD for BUILD_MODEL so that simple 3D interpolation
    can be used to generate undefined atoms; this reduces frequency of
    knots and insertions modeled in extended conformation.
  - Corrected the bug in parallel SHEET restraints, pointed out by
    S. Grzybek (rsrsheet). Also changed the specification of sheet
    restraints to allow complete control, by introducing ATOM_IDS
    and SHEET_H-BONDS TOP variables.
  - Corrected the inconvenient specification of atoms in ADD_RESTRAINT,
    DELETE_RESTRAINT, and in the restraints file in the USER format:
    Now using new atom id specification,
    ATOM_IDS: atom_name:residue_id[:chain_id].
  - Added improper dihedral angles to top.lib to ensure more planar sidechain
    rings.
  - Added the ability to write restraints in the USER format (selected via the
    RESTRAINTS_FORMAT TOP variable), not only to read them.
  - Modified WRITE_DATA command to add curvature and secondary structure output.    Removed separate options for writing to the output files and to the fourth
    column of the MODEL data structure.
  - Added the possibility to specify FILE in READ_MODEL with the second scalar
    in MODEL_SEGMENT. The same for READ_MODEL2.

Combined AS and RS version of Modeller 4: 05-10-1996
  - RS changes (general):
    - Added reduced model representation based on Herzyk & Hubbard (1993)
      Proteins 17: 310-324, but using three types of C-alphas for residues
      with helical, strand and turn propensities.
    - Added reading and handling of parameter files in modeller restraint
      format.
    - Added new RESTRAINT_TYPE : MRFP_STEREO, MRFP_BOND, MRFP_ANGLE,
                                 MRFP_DIHEDRAL, VDW14
    - Added options to read multiple parameter and/or topology libraries;
      ADD_TOPOLOGY and ADD_PARAMETERS options in READ_TOPOLOGY and
      READ_PARAMETERS, respectively.
    - Changed the atom type indexing to allow reading of multiple topology
      files and topology files containing only a subset of atoms. This forced
      changes in several places (check the headers of models.lib and rdrtop() ).
  - RS changes (detailed):
    - Changed models.lib and radii.lib to include the reduced model (model #9).
    - Added radii14.lib, it contains radii for 1-4 interactions (used for
      model #9).
    - Added topology and parameter libraries for reduced model:
      - top_ca3.lib : RTF for C-alphas in reduced model (no sidechains)
      - tophh.lib :  RTF for complete reduced model (C-alphas + sidechains)
      - par_ca3_spl.lib : Parameters for C-alphas in reduced model (this file
                          is in modeller restraint format)
      - parhh.lib : Parameters for sidechains from the Herzyk & Hubbard model
    - Changed rdparf() to add the ADD_PARAMETERS option which allows to read
      more than one parameter file. Added the MRFP keyword for parameter
      files in modeller restraint format.
    - The parameters in modeller restraint format read by rdparf() are stored
      in a common structure defined in param.cmn, the corresponding constants
      are defined in mod.cst.
    - Changed getrsr() to add new RESTRAINT_TYPE for MAKE_RESTRAINTS. The new
      types are MRFP_STEREO, MRFP_BOND, MRFP_ANGLE, MRFP_DIHEDRAL, and VDW14.
    - Added new routine mrf_stereo() which is equivalent to stereo() but it
      handles restraints in modeller format. The routines mrf_addcrs(),
      mrf_addcs() and mrf_ifndprms() are equivalent to addcrs(), addcr()
      and ifndprms(), respectively.
    - Changed rdrtop() to allow reading of multiple residue topology files.
      These forced the changing of atom type indexing as explained in the
      headers of rdrtop() and radii.lib. Basically CHARMM atom types are
      not considered anymore and RADII_LIB dictates the number of residues
      types and atom types. All atoms in the residue topology library must
      be defined in RADII_LIB which dictates the atom type index.
    - The number of residue topology libraries in memory is kept in nrtl, which
      is defined in topol.cmn.
    - Changed act56: removed check for consistency when reading a topology file.
      Consistency is now checked in rdrtop() by comparing the topology library
      with the entries in RADII_LIB.
    - Added RESTYP_LIB format check to inires().
    - Changed ID2 output format from i2 to i4 in gennam2().

Modeller 4 initiated: 04-12-1996
  - Added secondary structure assignment routine to WRITE_DATA and
    added the selection of output in WRITE_DATA by OUTPUT.
  - Deleted most of .mat files and several other un-needed files in modlib\.
  - Renamed GENERATE_MOLECULE to GENERATE_TOPOLOGY in several places.
  - Added the COLOR_ALN_MODEL command that colors a structure according
    to equivalences, insertions, and deletions in the aligned sequence.

Modeller 3c released: 04-11-1996

03-06-1996:
  - Added WRITE_WHOLE_PDB for MALIGN3D.
  - Corrected bug in __refine.top: TO-BE-REFINED.TMP
  - Corrected bug in compare() that did not write comparison matrices
    when ALIGN_CODES was empty.
  - Corrected a bug in rdaln() so that the sequences without pending gaps '-'
    also have gaps removed if so selected with REMOVE_GAPS.
  - Corrected a bug in selatm() which made RESIDUE_TYPES = 'HET' ignored.
  - Corrected a bug in schedule.lib which made hydrogen bonding group
    of restraints ignored (e.g., produced by RESTRAINT_TYPE = SHEET, HELIX).
  - Corrected a bug in build.F(getijk) found by Lisa Yan (natmpt-1) that could
    interfere with building initial coformation.
  - Corrected a bug in mod2ali that resulted in null characters at the end
    of shorter sequences in the alignments constructed by SEQUENCE_TO_ALI.

Modeller 3 released: 02-11-1996

11-03-1995:
  - Greatly improved the manual. Have the HTML version, too.
  - Changed GENERATE_MOLECULE --> GENERATE_TOPOLOGY
            MAKE_TOPOLOGY     --> MAKE_TOPOLOGY_MODEL
  - Added RENAME_SEGMENTS command and SEGMENT_IDS argument for
    automatically generating reasonable chain ids and residue
    numbers for multi-chain systems.
  - Changed the schedule for variable target function method
    and added schedule library.
  - Changed the residue specification in MODEL_SEGMENT, MODEL2_SEGMENT
    and SEARCH_SEGMENT so that #RES:C is used where #RES is residue
    number and C is the single character PDB chain id.
  - Added the symmetry term to the objective function (DEFINE_SYMMETRY
    command).
  - Added check for existence of Cys-Cys pair in target in PATCH_DISULFIDE.
  - Debugged, changed, and optimized  conmin() code for conjugate gradients.
    Removed Newton-Raphson method. Changed UPDATE_DYNAMIC from a single
    axis shift (0.23A) to 3D shift (0.39A) (top.ini, movsiz() and md2()).
  - Modified wrpap and rdpap so that they can read Insight alignment files too.
  - Optimized the generation of restraints a lot. Introduced SPLINE_ON_SPOT
    logical variable to save space. Saved lots of space by using splines
    instead of multiple gaussians.
  - Removed KEEP_DUPL_RESTRAINTS variable.
  - Added CHECK_ALIGNMENT command.
  - Added DEFINE_SYMMETRY command.
  - Added generic HET residue type for PICK_ATOMS.

09-10-1995:
  - Added check for SG atoms involved in more than one Cys-Cys bond.

08-07-1995:
  - Corrected a number of bugs found by Andras Szilagyi: MALIGN --> ALIGN
    in __align_strs_seq.top; MALIGN3D within TRANSFER_XYZ; a few manual
    mistakes.
  - Changing TAB to BLANK in the .top files.

07-04-1995:
  - Cleaned the calculation of the objective function, collected routines
    in one place: featpdf, objfunc, ...
  - Removed the pre-calculation of the violations and saved some space
    by deleting the corresponding arrays.
  - Changed the way the scaling is done: objective function terms and
    their derivatives are scaled directly, the restraint parameters
    are kept constant.
  - In PICK_RESTRAINTS, removed the selection criterion relying on the
    scaling factors of the current schedule.
  - Cleaned the output of the REPORT command.
  - Removed the calculation of many different kinds of violations on
    demand (relative, absolute, minimal, heavy). The relative
    heavy violations are used in PICK_HOT_ATOMS and REPORT.
  - Modified TOP scripts to use cubic splines if so selected instead of
    poly-Gaussians.
  - Added GDP and GTP residues to the topology and parameter files.
  - Added checks for undefined jumps in all computed GO TO statements.
  - Added automatic generation of stereochemical parameters from
    the current structure, for bonds, angles, torsions, and
    impropers that do not have an entry in the PAR.LIB file.
  - Automatically determines the type of the input restraints file.
  - Added BLK residue type for modeling residues without RTF entries.
  - In SEQUENCE_SEARCH, using one file with all sequences (SEARCH_CHAINS_FILE).
    Added SEARCH_CHAINS_LIST which is the same as the previous
    SEARCH_CHAINS_FILE.

05-17-1995:
  - Increased maxngh from 30 to 50 to allow for buried HEME groups (Mike
    Sutcliffe).
  - Increased mcnsres from 100 to 200 to allow for FAD (Mike Suctliffe).
  - Corrected the RAND_SEED = ISEED error which resulted in always
    the same randomization of coordinates by RANDOMIZE_XYZ (the models
    only differed because of the last MD part).
  - Corrected a bug that replaced a strong stereochemical SG-SG disulfide
    distance restraint with a weak SDCH-SDCH distance restraint based
    on a homolog if that distance existed in a homolog (csrdst()).
  - No more local optimization of sidechain dihedral angles in _refine.top
    because there are sidechain distance restraints.
  - Changed version number from 13 to 3.
  - Added INDEX option to STRING_IF.

04-29-1995:
  - Cubic splines transformation added for the poly-Gaussian restraints.
    This should speed up the execution and also allow using any number
    of templates without speed decrease. Also, should be more robust
    for optimization.

03-29-1995:
  - CONMIN changed to make it more robust with respect to precision 'problem 1'.  - SEQUENCE_SEARCH changed to allow writing out alignments.
  - Corrected chi2 and chi3 spec for PRO in resdih.lib.
    Corrected PRO pucker in resdih.lib and par.lib
  - Introduced 'user_after_single_model' TOP routine so that some action
    can be done by user after each model is calculated.

Supplementary Modeller12 release: 03-11-1995

02-15-1995:
  - Small changes to sys.F.
  - Free format for residue and chain ids in the alignment files (RDPIR()).
    Also, only the first 6 fields now necessary. Improved the description
    of the alignment file format in the manual.
  - Added rotation around axis to ROTATE_MODEL and changed
    the rotation matrix multiplication to make it consistent
    with QUANTA and MOLSCRIPT.
  - Added SUPERPOSE_REFINE to SUPERPOSE.

Modeller12 release: 02-01-1995

01-18-1995:
  - Changed divide() to divide2() in various *.F files, N-O distance cutoff
    from 15 to 12A, and SDCH-SDCH cutoff from 6 to 5 A (__homcsr.top) to
    speed up the execution.
  - Changed strnum2.F name to string.F
  - Eliminated SIGNIF2 output in SEQUENCE_SEARCH for now.
  - Added directory modelib/pdb/chn to the distribution. It contains about
    600 representative PDB chains from the 3.0_30_XN list. These chains
    can be used for template search by SEQUENCE_SEARCH. Modified
    Makefile.install1 to install this directory, too.
  - Recalculated the representative sets with the PDB version of January 18.
  - Made SMALL version of MODELLER even smaller.
  - Changed Makefile.include1 so that MODELLER12 runs fine in double precision
    on HP 9000/735 machines. HP's seem to have a problem with the size of the
    executable when there is not enough free memory. For this reason, Install
    still compiles MODELLER in single precison. Even in single precision, RSIZE
    is about 90MB.
  - Edited the manual; added sections on dynamic programming and comparative
    modeling primer (also in tests/primer).
  - Cleaned the tests/* directory a little.
  - Checked the official release 12 for MSI and others. Tested MODELLER on 18
    families from ALBASE3 (test_modeller12).

12-29-1994:
  - Changed rdpdb() and rdseqpdb() (in rdpir) to interpret @@@@@ and @
    strictly as any residue number and chain id, respectively.
  - Introduced HELIX, STRAND and SHEET restraint types in MAKE_RESTRAINTS.
    Not tested thoroughly.
  - Introduced 'GRASP' atom file format for WRITE_MODEL(2).
  - Introduced radii and radii2 vectors for MODEL and MODEL2.

12-20-1994:
  - Changed the default MAXRES from 400 to 600 and cutoff standard deviations
    in __refine.top from 3 to 4.
  - Reorganized the src directory to remove unnecessary programs.
  - Added OFF_DIAGONAL, OVERHANG, LOCAL_ALIGNMENT to ALIGN, ALIGN3D,
    MALIGN, MALIGN3D, and SEQUENCE_SEARCH. Corrected a bug in the
    alignment routines to do with long gaps.
  - Added logical ALIGN_ALIGNMENTS to ALIGN command.
  - Added READ_ALIGNMENT2 and COMPARE_ALIGNMENTS commands.
  - Added variables ALIGN_BLOCK and ALIGN_ALIGNMENT to the WRITE_ALIGNMENT
    command so that residue conservation can be indicated for an alignment and
    an alignment of two alignments.
  - Added ALIGN_CONSENSUS command.
  - Added alignment accuracy from ALIGN_CONSENSUS to be written out
    by WRITE_ALIGNMENTS in 'PAP' format if ALIGNMENT_ACCURACY = on. Also,
    absolute conservation of residues is always indicated by '*' in the
    'PAP' format.
  - Added optional version line to .rsr files (both formats).

11-15-1994:
  - Added strgin() function for unified processing of string options (case
    insensitive).
  - Made a major change in the restraint .rsr file format. The new format
    is incompatible with the old one, but it was necessary to deal with
    the NMR restraints, restraints on gravity centers, etc.
  - A new USER restraint format introduced. Introduced new TOP variable
    RESTRAINTS_FORMAT to select between MODELLER and USER restraint formats.
  - Added several new tests directories to test new features.
  - Added two new physical restraint types for NMR distance restraints.
  - Added a new command PRINCIPAL_COMPONENTS for protein clustering.
  - Cleaned and changed WRITE, READ, OPEN commands.
  - Cleaned io.F.
  - Introduced protected primes \' intro string values.
  - Since the 'homol' script has become so general, it was renamed to 'model'.
  - .csr extension for restraint files changed to .rsr extension.
  - KEEP_DUPL_RESTR variable added to READ_RESTRAINTS command, too.
  - Makefile.include1 improved (mkdir / mkdir -p selected as appropriate).
  - Introduced STRING_IF TOP command for IF on STRING_ARGUMENTS.
  - Changed __getnames.top to allowed user specification of the filenames
    for the initial model and restraints.
  - Changed TOP variable VDW_NEIGHBOURS to CONTACT_SHELL.

10-29-1994:
  - MODELLER12 upgrades started.
  - Built the dih.F, ngh.F, and psa.F functionality in MODELLER. Calculation
    of these derivative data only on demand and when not already in memory.
  - Added a bi-dihedral feature for Phi and Psi dihedrals -- a new binormal
    restraint. This restraint type really improves the Ramachandran plot
    quality of the models according to Procheck. It is ideal now. Unfortunately,    the binormal mathematical type can only be applied to dihedral angles,
    not to any feature type (distance, angle) because an assumption is made
    about the order of atoms in the 8-atoms list for this feature.
  - Least-squares fitted the multi-binormal Phi/Psi distributions in
    the database of approximately 440 representative X-ray (<2.3A)
    protein structures to obtain the new means, standard deviations
    and cross-correlations for Phi and Psi multi-binormals. These
    are stored in the new library MNCH2_LIB.
  - The omega dihedral changes to par_heav.lib are now not necessary anymore -
    they were needed in version 11 because par.lib applies to hydrogen
    topologies only and the omega restraint was weak - because omega dihedrals
    are restrained explicitly using the homologs and MNCH.LIB where
    appropriately strong omega restraints are specified. The original par.lib
    is therefore used again.
  - Added SDCH-MNCH and SDCH-SDCH distance restraints for equivalent atoms
    using the new ATMEQV.LIB library. This really helps positioning
    sidechains according to the template --- before the sidechain
    dihedral angle preferences frequently missed that. Now, if the template
    has the same sequence as the target, the model is almost the same
    as the template (only a few sidechains may differ a little).
  - Artificially increased the standard deviations close to gaps for
    0.6*(igap-4) in stdev() because I noticed that stereochemistry close to
    gaps is frequently distorted, presumably due to too strong CA-CA and N-O
    restraints.
  - Increased the number of restraint groups to 27 to allow for new distance
    restraints (SDCH-MNCH, SDCH-SDCH, protein - prosthetic groups).
  - PICK_ATOMS command was updated to allow it to define three different
    sets of selected atoms, selected by a new TOP variable PICK_ATOMS_SET.
    The three sets are used for different purposes.
  - Homology distance restraints derivation is improved a lot. Atom scanning
    for generating atom pairs is much more flexible: all pairs of atoms from
    selected sets 2 and 3 (as defined by the PICK_ATOMS command) are generated
    that are within the residue span range specified by RESIDUE_SPAN_RANGE.
    The meaning of RESIDUE_SPAN_RANGE is changed, too (a vector of 4 scalars
    now). Also changed RESTRAINT_STDEV which now specifies the linear
    transformation for ANY standard deviation for all 7 standard deviation
    models (s' = a + b*s).
  - A new command WRITE_DATA is introduced which writes out the PSA, DIH, and
    NGH files for the current MODEL. This is to outphase the psa.F, dih.F,
    and ngh.F programs completely. Note that the solvent accessibilities
    are slightly different because the atom radii are slightly different
    since the RADII.LIB is now used as opposed to PSA.DAT.

Modeller 11 release: 10-01-1994
  - Added many similarity matrices for sequence comparisons obtained from FASTA
    distribution, Mark Johnson, and David Wishart (seqsee). It was shown by
    Feng Yuan that my matrix as1.sim.mat is the best for remote homology
    searches.

09-24-1994:
  - Simplified TOP <--> APPLICATION variable copying.
  - Introduced CONTROL variable, which controls the stop status and
    the amount of output written to the log file.

09-13-1994:
  - Added catching of the undefined atoms in PSA.F to prevent the crashes.

09-01-1994:
  - Added the TOP variable FILE_EXT and modified gennam() so that FILE_EXT
    is added to all deault filenames. Now MSI can append '.modlr.pdb' to the
    output B filenames.
  - Changed __*.top scripts to write out the final models in the form
    pdbcode.B9999nnPDB_EXT. Made all the test cases consistent with it.
  - Added the TOP variables FILE_ACCESS and OUTPUT_DIRECTORY. Consolidated
    input and output directory handling.

08-24-1994:
  - Changed many scripts/__*.top scripts to allow more flexible 'homol'
    use: using pre-existing initial model or restraints files, exiting during
    various stages of 'homol', and flexible specification of optimization
    thoroughness. See file scripts/__defs.top for the options.

08-23-1994:
  - A bug that set nseq=2 in seqsearch() corrected.

Modeller 10 release: 08-17-1994
  - Created the anonymous ftp on tammy with the en-crypt-ed tar file.
  - Added the OMEGA dihedral angle restraint type to MAKE_RESTRAINTS.
    This now allows automated cis/trans restraints to be derived
    for proline residues, according to the ALBASE paper (Sali & Overington,
    Prot. Sci., 1994). Several other changes had to be made mainly
    to the csrdih() and getcsr() routine to make this work. The top routine
    __cispeptide.top is now almost irrelevant, unless you still want to
    restrain some peptides manually; i.e., the cis/trans Pro restraints
    are derived automatically by CALL ROUTINE = 'homol'.
  - TOP variable BASIS_RELATIVE_WEIGHT was added to allow better reduction of
    poly-Gaussian restraints.
  - Created PATCH_DISULFIDES command which automatically derives disulfides
    for MODEL from its sequence and disulfide presence in aligned structures.
  - Also changed __*.top scripts so that Chi3 and Chi2 homology-derived
    restraints for S-S bonds are calculated together with other Chi3 and
    Chi2 restraints in __homcsr.top: disulfide restraints are derived
    automatically by CALL ROUTINE = 'homol' if there are equivalent S-S
    bonds in any of the templates; for unique S-S bonds the top routine
    __special_patches still has to be created manually.
  - Re-calculated all sidechain and mainchain *.mdt and *.bin files using
    ALBASE_3.
  - Added the calculation of the significance score to the SEQUENCE_SEARCH
    command; regulated by the new top variable SEARCH_RANDOMIZATIONS.
  - Checked all tests\* and consolidated/renamed some tests.

08-09-1994:
  - Included Phi, Psi, and Omega angles in the default refinement in
    __refine.top.

07-16-1994:
  - Added full-proof atom building capability to the build() routine.
    Atom always built, it is just a question what the coordinates are.
    This is usefule when IC entries not sufficient for building (e.g.
    only CA atoms available).
  - Added CHI5_DIHEDRAL type restraint to getcsr()/mdtcsr() and updated
    types.cst, TOP files in tests and scripts from 23 to 24 physical
    feature types to reflect this.

07-03-1994:
  - Added the SEARCH_SORT TOP variable for seqsearch().
  - Corrected small problems in Makefile to do with deleting Makefile.hosttype.
  - Improved ALIGN3D by adding the option of the Subbiah/Laurents/Levitt
    transformation of distances (ALIGN3D_TRF variable) and by allowing for
    three additional initial alignments (ALIGN3D_REPEAT variable).

06-25-1994:
  - Adapted Makefile and system() to run on CRAY C90.
  - Corrected a small bug in describe().
  - Corrected a serious bug in seqsearch() which caused wrong %ID.

06-14-1994:
  - Added the MUTATE_MODEL command to mutate model sequence easily.

06-10-1994:
  - Added the handling for the distribution of the executables only.
  - Added the ATOM_FILES_DIRECTORY TOP variable.

06-01-1994:
  - Corrected the S-S problem in the TOP scripts for homology modelling: the
    S-S bonds were forgotten when GENERATE_MOLECULE was executed again in the
    later stages of modelling without repeating the 'special_patches' call, too.

05-23-1994:
  - Corrected fmakedepend handling for automated dependency generation in
    Makefile.
  - Added install script to the root directory for easy interactive
    installation.
  - Clarified the roles of GENERATE_MOELCULE and READ_MODEL commands. Made
    appropriate changes to the code and to the tests/*.top files.
  - Introduced automated segment naming for PDB and CHARMM atom file I/O.

05-22-1994:
  - Added automated unique segment name generation to wrpdb2 for writing PDB
    files.

05-15-1994:
  - A serious 'TOP routine name duplication' bug corrected in top1.F (only
    had an effect when TOP routines were re-defined: e.g. __cispeptide,
    __disulfide).
  - The ELEC, ELEC14, LJ, and LJ14 restraint types added to MAKE_RESTRAINTS
    and cross-checked with CHARMM. Reading the second set of LJ parameters
    in the CHARMM parameter file for LJ14 implemented.
  - mkexcl() routine generalized and corrected: excluded atom pairs are
    derived from the list of bonds, angles, dihedrals, and explicitly excluded
    pairs; not from stereochemical restraints anymore.
  - BUILD generalized so that if the first three seed atoms do not result
    in all the coordinates built with the given IC entries, other seed atoms
    are tried. A bug in accic() corrected which sometime removed useful IC
    entries.
  - PMF (potential of mean force) routine added with TOP variable PMF_GRID.
  - TOP variable RELATIVE_DIELECTRIC added for ELEC and ELEC14.
    TOP variable PATCH_DEFAULT added for GENERATE_MOLECULE command.
    TOP variable INTERSEGMENT added for MAKE_RESTRAINTS command.
    TOP variable PMF_GRID added for PMF command.
  - TOP variable ADD_RESTRAINTS got a meaning for PICK_RESTRAINTS;
    adds the newly picked restraints if ADD_RESTRAINTS = ON.
  - New test top files added to tests/pmf and tests/energy_debug (vdw*, elec*).
  - Two new IC entries added to top.lib to allow BUILDing of individual
    residues without patches.
  - __homol.top modified so that exit after restraints calculation is possible.
  - __homol.top modified so that .csr file always calculated so that possible
    disulfide PATCH is always reflected in the template's topology arrays;
    before, S-S were also restrained by the non-bonded restraints. This
    could be done better with proper GENERATE_MOLECULE use.

05-01-1994:
  - OUTPUT = NO_ALIGNMENT option added to ALIGN3D and MALIGN3D.

04-22-1994:
  - __single_model.top corrected so that it did not boink out when no
    refinement was done and SCHEDULE_STEP was out of range for a subsequent
    energy evaluation (a bug discovered by Liz Potterton).

03-22-1994:
  - Added TOP variable RESTRAINT_STDEV which defines the standard deviation
    of the Gaussians when DISTANCE_RSR_MODEL = 7 in MAKE_RESTRAINTS.
  - Unified the numbers of residue types so that the MODELLER residue types
    close to 100 are recognized everywhere. The previous code sometimes
    recognized only the 20 standard residues.
  - Added tests/prosthetic/tst2.top to illustrate homology modeling with
    prosthetic groups.
  - Changed dih3.F, psa.F, and ngh1.F to write out the HETATM residues so that
    the .dih, .ngh, and .psa files have exactly the same sequence as the PDB
    files with HETATM.

03-17-1994:
  - Added QUANTA alignment format for READ_ALIGNMENT and WRITE_ALIGNMENT.
  - Added some arrays about segments in MODEL, MODEL2 and sequences in the
    alignment arrays. Not finished yet.
  - Added MALIGN3D and MALIGN, improved ALIGN, and ALIGN3D.
    Added TOP variable ALIGN_BLOCK.
  - Added scripts __full_homol.top and __align_strs_seq.top for
    homology modelling from a list of structures and a sequence only (all
    alignments are derived automatically).
  - Created tests/malign3d, tests/full_homol, tests/align3d.
  - Re-tested all tests/*.
  - Updated the manual to reflect the new changes.
  - Corrected the automatically derived top_ca.lib to allow BUILD to work.
  - Added SEQUENCE_TO_ALI command for copying MODEL sequence to alignment
    arrays.
  - Added top variable ADD_SEQUENCES for adding sequences/alignment to existing
    sequences/alignment.
  - Added TOP variable NUMB_OF_SEQUENCES.
  - Added TOP variables MODELLER_STATUS and STOP_STATUS to READ_ALIGNMENT and
    all the alignment routines. Updated the meaning of these for OPTIMIZATION.
  - Added an option in the ENERGY command that Biso column of the PDB file
    becomes the average residue violation (when OUTPUT='RESIDUE_VIOLATIONS')
    for displaying on the graphics screen.
