ProSMART changelog:

v0.841: 18/9/2014

change - updated default value of parameter (keyword: -restrain_score) from 0.6 to 0.8.

v0.84: 12/9/2014

feature - enabled use of all structural comparison and restraint generation functionalities with DNA/RNA chains (keyword: -dna_rna).
feature - improved rigid substructure identification method, which better utilises/penalises translational component rather than relying too heavily on rotational component, as well as trialling multiple parameter sets to account for different degrees of conservational variability. This is mirrored in the output "cluster" colour script files.
feature - screw axis-angle representation of rigid body transformations. These are calculated relative to original coordinate frame, and also corresponding to domain motion (i.e. for each identified substructure pair). These are implemented for global superposition, as well as for each cluster-pair. Rotation angle, signed screw translation magnitude, rotation axis, and screw origin are reported in the logfile. Calculation of screw axis-angle representation may be suppressed (keyword: skip_screw).
feature - output PyMOL scripts for visualisation of each of the screw axis-angle representations (in Superposition->Transformations).
feature - auto-removal of non-sensible chain-pairs from restraint generation. Introduced criteria that chains must satisfy in order to be used as reference models, on the basis of similarity to the target model. Specifically, chains must meet minimum sequence identity requirements (keyword: -restrain_seqid) after alignment, and structural similarity (net local RMSD) requirements (keyword: -restrain_score), the latter being determined from the net minimum/flexible score resulting from the structural alignment. Note that this may result in no restraints being generated for some chains.
feature - support for UCSF Chimera. ProSMART now outputs scripts allowing Chimera to be used for viewing the standard structure superpositions and colouring according to residue-based structural dissimilarity scores, similarly to as with PyMOL. PDB loader scripts are found in Output_Files->Loader_Scripts->Chimera - these load the PDB files and create named selections for target and reference structures (called 'prosmart1' and 'prosmart2'), and colour scripts are found in Output_Files->Colour_Scripts->[chain-pair-ID]->Chimera - these colour scripts assume that the PDB loader has been previously executed at the start of the session (due to requiring that the correct models have been tagged using the named selection method). Chimera scripts are not currently available for visualisation of hydrogen/generic bond restraints, nor screw axis-angle representation of structure transformations.
feature - enabled ability to remove atoms with occupancy less than value (default '0', i.e. remove atoms with zero occupancy) (keyword: -occup).
feature - ability remove side chain RMSD scores from residue alignment output files for residues that contain atoms with zero occupancy, alternative conformations, or side chains with missing atoms (keyword: -score_strict).
feature - ability to use side chain atoms (for sequence-identical residues) as well as backbone atoms when superposing structures (keyword: -superpose_side).
feature - ability to output additional alignment files (keyword: -output_rmsd) containing the RMSD of aligned backbone and side chain atoms relative to the global coordinate frame, as well as the coordinate frame of each identified rigid substructure cluster. These files are located in the Residue_Alignment_Scores subdirectory, despite actually relating to the atomic alignment.
feature - ability to use the sieve-fit procedure (Lesk, 1991) to post-process superpositions, allowing superpositions to be further tightened (keyword: -sieve). This applies to both the global and the rigid substructure cluster superpositions. The sieve-fit parameter, which specifies the final RMSD of atoms used for structure superposition, may be chosen (keyword: -sieve, default 0.5).
feature - output "max_dissimilar.txt" files in Residue_Alignment_Scores when comparing sequence-identical structures, whenever "-id" keyword is used. These alignment files contain maximum/worst scores observed over all performed pairwise comparisons.
feature - added extra info in external restraints files to aid identification of source. This info can subsequently be added to the header of any models re-refined using these restraints.
change - enabled -side keyword by default. ProSMART will now generate restraints for both backbone and side chains (unless -main keyword is specified).
change - enabled -restrain_best keyword by default. ProSMART will now only generate restraints for each target chain using the one reference chain that is identified as being most similar, in terms of net local structural similarity (unless -restrain_all is specified).
change - enabled -sigma_type 0 by default. ProSMART will now assign all restraint sigmas a fixed value (default 0.1) instead of attempting to estimate based on the distribution (unless -sigma_type 1 or -sigma_type 2 are specified).
change - ProSMART will no longer execute REFMAC5 to calculate atom-pairs related by a bond/angle by default, thus will not remove corresponding restraints by default (unless -rm_bonds, -sigma_type 1 or -sigma_type 2 are specified).
change - updated file names/descriptions and column headers in residue alignment output files, PyMOL colour scripts, global scores files, HTML output files, etc. in order to agree with recent Acta Cryst D article Nicholls et al. (2014).
change - merged PyMOL global and cluster-based PDB loader scripts - there is now just one script for each chain-pair, which contains both global and cluster-based superpositions.
change - moved PyMOL PDB loader scripts from Output_Files->Superposition->PDB_files to Output_Files->Loader_Scripts->PyMOL.
change - suppressed display of residues of unknown type ('X') in output sequence files.
change - implemented checks to determine whether transformations are near-identity, in which case identity transformation is used in order to overcome any numerical precision issues in the output.
change - Reduced number of console windows that temporarily appear when running ProSMART on Windows systems, no longer will there be a separate console window for each chain-pair.
change - removed unused TNT header files.

v0.83x: special versions - undocumented.

v0.822: 27/1/2014
special version - identical to v0.816 except for minor fix to TNT files to allow clang 5.0 compilation on Mavericks.

v0.817-0.821: special versions - undocumented.

v0.816: 4/7/2012
fix - issue on Windows when directory paths that don't contain spaces are specified in quotes.

v0.815: 15/6/2012
change - changed way in which parameters are altered when re-searching for rigid substructures, which should improve number of hits and rigidity. As a result, it is impossible for output cluster column to contain all NAs unless there are no identified substructures. Also allows two searches to be performed if required, instead of just one.
change - removed NumDist from alignment scores tables, by default.

v0.814: 7/6/2012
feature - Hybrid sequence-structure alignment procedure (to disable, use keyword: -no_reward_seq). Any fragment-pairs that are identical in sequence are assigned a favourable score (keyword: -reward_seq).
feature - Ability to compare oligomers/complexes as individual structural units (keyword: -merge). Specifically, merges chains within a PDB file, effectively converting all chains of interest (e.g. oligomers) into a single chain. Residue numbering is altered accordingly (warning - all results will reflect the renumbered residues, and will not refer back to the original numbering scheme).
feature - Outputs colour scripts corresponding to maximum dissimilarity on a chain-on-all basis when performing all-on-all structural comparisons.
change - PDB loader scripts for all-on-all comparisons now load the primary chain as well as secondary chains.
change - altered protocol of 'manual' installation for windows version. In fact, installation is no longer required. Specifically, ProSMART is runnable from original distributed directory (after unzipping).
fix - completely removed requirement for a specific temporary directory. This fixes issues with write permissions in CWD.

v0.813: 8/5/2012
change - improved makefile. Allows parallel compilation by default.

v0.812 : 26/4/2012
feature - automatic detection of nomenclature inconsistencies between atoms in sequence-identical side chain residues (for PHE, TYR, ARG, ASP, GLU, VAL and LEU). This is now accounted for by default when calculating side chain RMSD scores and colour scripts, etc. This is not currently accounted for in other functionalities, such as restraint generation.
feature - automatic detection of potential errors side chain conformation, given conservation of atoms in sequence-identical residues, by allowing side chain flips (for HIS, THR, ASN and GLN). This is now accounted for by default when calculating side chain RMSD scores and colour scripts, etc. This is not currently accounted for in other functionalities, such as restraint generation. This feature may be disabled (keyword: -no_fix_errors).
feature - allow specification of a directory containing all input files (keyword: -input_dir).
feature - added new PyMOL colour script "sidechainMAX.pml" to default output. This colours by maximum difference between corresponding side chain atoms in an aligned residue-pair, in the local coordinate frame (only for sequence-identical residues).
change - job now continues if there exist chains with no chain ID, instead of terminating. Such chains are skipped if encountered.
change - enabled processing of non-MSE synthetic residues.
change - unknown residue types are now denoted 'X' in output sequence files.
change - enabled ability to process atom element and charge records.
fix - issue with residue names in alignment files when encountering incomplete residues.
fix - issue with NH side chain atoms being overlooked.
fix - issue with fragment library due to change of directory name to "prosmart_data".
fix - issue with latest version of compiler gcc-4.7.

v0.811 : 5/4/2012
fix - issue with alignment file interpretation when generating restraints for library fragments.

v0.810 : 23/3/2012
feature - generic bond restraints (main keyword: -h or -bond). By default, this equates to main-chain / secondary structure hydrogen bond restraints. By default, these operate spatially, not in sequence.
feature - added several profiles for secondary structure hydrogen bond restraint types (keywords: -h_helix, -h_sheet, -3_10, -alpha, -pi).
feature - added ability to filter bond restraints by fragment type (helix and strand only at present) (keyword: -strict).
feature - added ability to customise restraint objective and detection values (keywords: -bond_dist, -bond_min, -bond_max).
feature - added ability to customise residue separation criteria for generic bond generation (keywords: -min_sep, -max_sep, -allow_sep, -rm_sep).
feature - added ability to override automatic atom-pair bond profiles. Three profiles added (keyword: -bond_opt).
feature - added ability to override maximum number of generic bond restraints per atom (keyword: -bond_override).
feature - new troubleshooting option (keyword: -troubleshoot_hbond_restraints).
feature - added two new output PyMOL colour scripts for visualisation of generic bond restraints - 'bond_residue_separation.pml' and 'bond_restraints_per_atom.pml'.
feature - added output PyMOL interatomic distance dash measurement script for visualisation of generic bond restraints (located in Restraints/Chain_Chain/).
feature - added PyMOL loader scripts that automatically load PDB files, colour scripts and interatomic measurement scripts with specific 'bond_residue_separation' and 'bond_restraints_per_atom' profiles.
feature - resurrected ability to output max_dissimilar alignment files and colour scripts for multiple identical structures and NMR/MD ensembles.
feature - added ability to generate generic self-restraints (keyword: -self_restrain). This feature is generalised to any sort of structural information - not just the polypeptide chain. This feature can be used to generate external DNA/RNA interatomic distance restraints using homologous structures (this feature requires homologues to be sequence-identical, i.e. enumerated with equivalent residue numbering and must have the same nomenclature for atom names. If the homologues are not sequence-identical then the restraints files will require post-processing for successful use). Automatic DNA/RNA restraints to non-identical homologues will be implemented as a separate feature in a future release.
feature - added "ANGLE_DIST" record to output transformation files. This specifies the angular and translation distance between the reference chain before and after superposition using the corresponding transformation. The angle directly corresponds to the "ROTATION" record. However, the distance doesn't directly correspond to the "TRANSLATION" record. Rather, the distance is the difference between the average of the coordinates of aligned residues' atoms before and after transformation.
feature - added MaxDist and NumDist to list of residue-based scores in the output alignment tables. These correspond to maximum interchain interatomic distance between corresponding atoms in the residue, and the number of atoms with interchain interatomic distance greater than some threshold.
feature - added ability to choose to also use main-chain N, C and O atoms when calculating the residue-based SideRMS, MaxDist and NumDist scores (keyword: -main_dist). Default is to use only CA and any side-chain atoms.
feature - added ability to choose the threshold for the NumDist score (keyword: -numdist). This score is the number of atom-pairs that have interchain interatomic distances greater than the threshold (default: 1.0).
change - changed source and installation directory structure, in order to match the structure in the bazaar repository. Thanks to Marcin Wojdyr for recommendations.
change - Allowed specification of data directory in makefile. Made specification of installation directories more flexible in Windows.

v0.809 : 29/2/2012
feature - allow specification of different restraint types (keyword: -type), specifically bond type restraints (replace existing), bond type restraints (add to existing), and external restraints (as default).
feature - can specify for output superposed PDB files to contain all chains present in the original PDB file, instead of just the chain of interest (keyword: -out_pdb_full).
change - output superposed PDB files now contain all atoms (e.g. including Hydrogens, heavy atoms, ligands) that have the appropriate chain identifier.
change - extensive technical changes to the code, including reduction of code divergence between Unix and Windows versions, increased conciseness and reduced duplicity, and avoiding the use of shell scripts. Thanks to Marcin Wojdyr for recommendations.

v0.808 : 14/2/2012
feature - outputs residue-based alignment files for identified rigid substructures (or clusters). The file contains angular dissimilarity scores for each residue, compared with each identified rigid substructure. Also, independently, residues are discretely assigned to the closest cluster, or to no clusters (depending on the chosen degree of final cluster rigidity; keyword: -cluster_rigid).
feature - can specify for intrafragment rotational dissimilarity scores to be displayed as cosine distances (instead of angular degrees) in the residue-based alignment and cluster alignment files (keyword: -cosine). Using this keyword may result in a minor speed increase.
change - in standard residue-based alignment files, the intrafragment rotational dissimilarity score is now reported as an angle (degrees) by default, instead of as a cosine distance.

v0.807 : 11/2/2012
feature - by default, final restraints files are now copied to the ProSMART_Output directory (although this can be disabled, to save storage space, by using the keyword: -no_copy).
change - general improvements to user-friendliness of configuring custom installations.
change - removed necessity for specification of ROOT_DIR.
change - removed necessity for specification of TMP_DIR.
change - various technical improvements to IOF operations.
fix - increased installation flexibility and syntax support, allowing easier local installation in home directories on Unix-based systems.

v0.806 : 30/1/2012
fix - issue with creating output PDB files when input PDB files include very long lines.

v0.805 : 23/1/2012
feature - option to output PDB_Chain restraints files (keyword: -output_pdb_chain_restraints). These comprise restraints for all chains in the target structure using only one of the secondary reference chains. One PDB_Chain restraints file is created for each of the secondary reference chains.
feature - new troubleshooting option (keyword: -troubleshoot_restraint_files).
change - disabled default generation of PDB_Chain restraint files (these files were rarely used, and can take up a lot of disk space).
change - disabled generation of "max_dissimiar" alignment files and colour scripts, which were only generated for sequence-identical structures and NMR/MD ensembles. These may be easily re-enabled at a later date.
fix - issue with "-id" keyword.

v0.804 : 18/1/2012
feature - Windows version made available.
feature - allow nested keywords files (keyword: -f).
change - increased flexibility of input file specification.
fix - issue with residue-based scoring in ProSMART RESTRAIN (currently unused feature - necessary fix, but this will not affect any restraints generated by users in any way).

v0.803 : 13/1/2012
feature - ability to specify residue ranges, so that only portion of PDB files may be used during alignment (applied during PDB file processing) (keyword: -align).
feature - ability to remove specific residues (applied during PDB file processing) (keyword: -align_rm).
change - various minor changes to presentation of main runtime log.
change - empty alignment files (and score files, etc.) are now outputted if the alignment is of length zero.
change - rigid substructure identification is no longer attempted if there are insufficient aligned fragment pairs to possibly achieve any substructures.
fix - issue with low score filtering.