V0.1 25.09.92 Original V0.2 02.10.92 Added CURSES support V0.3 07.10.92 Added Amiga windows and paging support V0.4 09.10.92 Added N&W alignment support & fixed bug in multi-zones V0.5 08.10.93 Various tidying for Unix & chaned for booklib V0.6 05.01.94 Modified MDMFILE for Unix getenv() More tidying Reads HELPDIR and DATADIR environment variables under V0.7 24.11.94 Uses ReadPDBAtoms() The DATAENV environment variable is now handled by code in bioplib/align.c/ReadMDM; Checks the return from ReadMDM(). Fixed bug in multi-zone align. Some ammendments to ProFit.help to explain the use of chain names in ZONE specifications. V0.8 17.07.95 Fixed bugs in multi-chain fitting. Chain name must come *before* residue number. Removed windowing code. V1.0 19.07.95 Allows inserts in structures including insert names in zones. Allows HETATM records to be included. HETATMs are not read by default. However, by putting a -h on the command line, or giving the HETATOM command you may get ProFit to read HETATM records. The extraction of sequence now ignores HETATM records, so the problem with the ALIGN command when there were HETATMs should have gone away. There is now a RESIDUE command which gives a by-residue RMS over the current RATOMS and RZONE (ATOMS/ZONE if RATOMS/RZONE unspecified). If you are reading commands into ProFit from a file rather than from the keyboard, you no longer get loads of ProFit> prompts appearing in your output which tidies things up a bit. An end of file also ends the ProFit program, so you no longer *need* to put QUIT in the command file. V1.1 20.07.95 Added WEIGHT/NOWEIGHT commands Added translation to MATRIX output V1.1a 21.07.95 Fixed core dump when trying to write unfitted file V1.2 22.07.95 Added GAPPEN command 25.07.95 Added printing of chain labels in Status Bioplib's three->one translation now handles nucleic acids. RESIDUE command takes optional filename parameter to direct output to a file. V1.3 31.07.95 Fixed bug in ZONE command when end of zone=end of chain which was not the last chain. Prints number of residues in zones when a mismatch occurs. Potential out-of-bounds memory access fixed in weights array. V1.4 14.08.95 Fixed printing by residue which was not printing the last residue. V1.5 21.08.95 Fixed bug in creating zones from NW alignment when last zone != end of chain. Also fixed bug in Bioplib/align.c which was messing up the end of an alignment. 24.08.95 Fixed a bug in Bioplib/align.c which caused potential core dumps when an amino acid type not in the MDM matrix was found. This should never cause a problem in ProFit since these junk characters are never generated. -------- 27.09.95 Updated profit.hlp which still said insert codes are not allowed in ZONEs V1.5a 02.10.95 Added centre of geometry data to output of the MATRIX command and updated profit.hlp with this information. V1.5b 15.11.95 Prints score normalised by shorter sequence length as well as matrix maximum score. Updated profit.hlp which said numeric zones could be specified as a single residue. V1.6 20.11.95 Added READALIGNMENT command. -------- V1.6a 21.11.95 Fixed a couple of warnings under gcc V1.6b 22.11.95 Modified code in SetNWZones() such that deletions at the same position in both sequences don't cause a problem. This was only a problem if an alignment was read using READALIGNMENT which had a deletion in both sequences. V1.6c 13.12.95 Fix 1.6b wasn't working if a double deletion occurred in the middle of a long run of deletions V1.6d 24.01.96 Fixed bug in STATUS command when atom names contain spaces. Modifications to docs. Error reporting improved: no atoms read from PDB files distinguished from no memory. Fixed bioplib bug in converting an all HETATM file to sequence. V1.6e 31.05.96 Added BVALUE command V1.6f 13.06.96 Added BWEIGHT command V1.6g 18.06.96 Internal changes only --- replaced FindZone() by FindZonePDB() in Bioplib V1.7 23.07.96 Some tidying of comments Fixed potential out-of-bounds array errors in atom specifications Added atom wildcard specifications -------- V1.7a 06.11.96 Added -ve values for BVALUE Added IGNORE/NOIGNORE V1.7b 11.11.96 Added REF and MOB options to BVALUE keyword to allow only one to be examined rather than an average V1.7c 18.11.96 Added IGNOREMISSING option V1.7d 20.12.96 Added NFITTED command Fixed a bug in bioplib/ReadPDB() which would cause completely blank lines in a PDB file to produce data from the previous line. V1.7e 27.06.97 Added ability to output from RESIDUE and WRITE to a pipe. V1.7f 03.07.97 Added break into CreateFitArrays() to fix core dump on bad multiple-occupancy PDB files. If the 'same' atoms don't appear immediately next to eachother (they should), then all are read by ReadPDB() and this routine was then comparing all with all. Also warns of multiple occupancies on reading file. Changed to use CD1 for ILE rather than CD. V1.7g 06.05.98 Complete rewrite of NWAlign/SetNWZones(). The new version is much simpler; it also fixes a bug which occurred following 1-residue zones. V1.8 07.05.98 Release of V1.7g -------- V2.0 01.03.01 Added support for multiple structure fitting and iterative zone updating. Output atom names now exactly match input names. Can write coordinates with centre of geometry of fitted region at the origin. Added QUIET option. Added LIMIT command to restrict region read from an alignment to create fitting zones. V2.1 28.03.01 Added cutoff parameter for ITERATE and added CENTRE command V2.2 20.12.01 Fixed some Bioplib problems related to raw atom names and multiple occupancies --------